Just some factual details to straighten out first before going to your answer:
First, the intake valve does NOT instantly close at BDC. Even the gsr cams have 40 degrees after BDC before they close. The wilder cams take even longer after BDC to close. Why? because we don't have F1 pneumatic or electromagnetic valve actuaters. We use valvesprings which don't instantaneously open and close a valve (like a square wave pattern...on/off switch). The valve isn't slammed onto the valve seat too hard to cause valve bounce. In wilder cams, higher intake lift dictates the need for longer intake duration. Now, this ABDC valve closure period is where we lose vacuum/cylinder pressure/(dynamic) compression even if the rings are good (dynamic compression is affected by late intake valve closure). The later the intake valve closure is an attempt to capture some more intake mixture using the "ram effect" (see the Ramming the Rat Article from Hot Rod 1999 that I quoted in one of the IM design threads here). However, the mix is being compressed in these 40 or more degrees and the path of least resistance is back up the intake port. We won't get into the balance between the exhaust cam duration relative to the intake cam's duration and LSA today.
Secondly, anything above 1.65 rod ratio is considered good and still "high". 1.66 is NOT low. "Ideal" is 1.75-1.77. You get into powerbands that are located to high and too narrow to be useful once you exceed 2.05:1 and would require a 7 speed, close ratio gearbox to keep you there in that powerband.
Now, onto cylinder filling.
cylinder filling is a function of port volume/flow capacity, efficiency (loss from friction or pumping losses), IM design, intake valve size and the number of intake valves (4-5 valve head vs 2 valve head), cam profile, rpm, bore size relative to rod ratio, and displacement.
Let's deal with some of these factors in sequence.
In terms of port size/flow capacity, displacement, efficiency, rpm, and displacement....In a 1.8L (110 cubic inches) with 8000 rpm redline, you have:
110 cu. in. x 0.5 = 55 cu in. per revolution
[55 cu in/rev]/ 1,728 = 0.032 cu. ft/ rev.
0.032 cu. ft/rev x 8000 rev/ min. = 254 cu. ft./ min. (cfm) flow needed to fill the cylinder.
This is the port flow capacity you need to fill the cylinder at 100% efficiency (no viscous or pumping losses).
Now, port volume as it relates to filling only and rod ratio:
The relationship between rod ratio and port size goes un-noticed by a lot of people. Low rod ratio engines like larger "lazy" ports, moreso than high rod ratio engines. This combination of low rod ratio piston geometry and big ports biases the powerband gains towards the upper rpm range.
If you look at a stock B16a head it has smaller port sizes. When you combine that head made for a high revving high rod ratio motor and put it on a low rod ratio block like a B18B (1.54 r/s ratio), the midrange torque is phenomenal. The LS/VTEC's combination of high piston speeds early after TDC from a low rod ratio and smaller ports for higher flow speeds will fill the cylinder at low rpms better.
We already know that in a 2 stage IM, the resonance frequency increases when the secondary butterfly valves open and this creates a second sonic wave that provides higher pressure arriving at the intake valve as it opens. This 2 stage IM idea assists in cylinder filling but at the cost of added flow drag. Initially the 2nd stage of a 2 stage IM improves upper rpm power but at higher and higher rpms, the added drag from the additional runners begin to cancel out their advantage on filling (poorer flow quality).
We haven't said a word about flow quality yet, up to this point. Filling the cylinder as much as possible (quantity) versus obtaining a stratified charge in the cylinder (quality) are separate but equally important issues. It's not only mixture quantity but also mixture quality for a more complete fast burn that gains power.
Flow quality as the mix enters at the valve seat can be affected by the initial energy of the flow from the time the intake valve opens to about 12-14 degrees afterwards and can be affected by the valvespring rate and intake cam lobe's shape/grind (ramp angle) which dictates the speed at which the intake valve opens. The critical initial speed is what helps completely fill the cylinder. You not only want to fill the cylinder with the volume of mix needed for the level of power wanted but you also want to stratify charge inside the cylinder. We already mentioned valve seat angles and people use different strategies to help fill the cylinder in an article already (enhance low lift flow or don't enhance low lift flow for antireversion).
You do not want any swirling of the mixture to happen in the port above the valve seat. The mixture should approach the short turn radius at speed, slow down to make the bend, enter past the valve seat, and then swirl fill the cylinder. It is critical that the mix is then pushed over by the rising piston, on the compression stroke, over to the exhaust side of the cylinder to regain speed and induce stratification. Stratification in a compact combustion chamber ensures complete burning of the mix...making power.
You'll notice the dome shapes on the pistons for N/A monsters all have deeper valve pockets on the exhaust side compared to the intake side and that there is a slope deep into the piston dome from the intake side down to the exhaust side. The piston is the "floor" of the chamber and this "floor" is rising up, as it compresses the mix. This squeezing action and the shape of the dome compresses AND pushes the mix towards the exhaust side.
The last thing to consider is bore/rod ratio combinations. Honda chose a small bore with the higher rod ratio motors. A shorter stroke with a smaller bore will make torque in the midrange. The D series motors with 1.6L can smoke a B16a 1.6L in the midrange (all other things being equal).
With the basics out of the way, back to your question.
If we have the same small port size, 1.8L displacement, 8,100 rpm redline, IM, cams, valve seat angles, intake valve size & number, bore:
The higher rod ratio engine, the faster the piston speed further away from TDC or "later down the intake stroke" in filling. The lower the rod ratio, the faster the piston speed earlier on the intake stroke or closer to TDC.
A high rod ratio engine has more piston speed earlier going away from BDC. In contrast, a low rod ratio has lower piston speed away from BDC, relatively speaking.
You are correct in thinking that piston speeds can dictate filling. Since rod ratio determines piston speed and where the max piston speed occurs, it is oNE factor among many that will dictate filling.
Here's a formula for exact piston position (inches of stroke) for crank position in degrees:
SE = (S ÷ 2) + R + [(S ÷ 2) × cosA] - SQRT [(R2) - ((S ÷ 2) × sinA)2]
where "SE" is the effective stroke, "S" is the nominal (full) stroke, "R" is the rod length, "A" is the crank- shaft angle in degrees ABDC from 0 to 90°, and "SQRT" (or "SQR") is the square root function. to convert from degrees to radians:
Radians = Degrees × .017453, or Degrees × Pi ÷ 180.
A simpler equation but only for maximum piston speed:
Z = N2 × S (1 + (1 ÷ 2n)) ÷ 2189
where "Z" is piston acceleration in feet per second squared, "N" is engine RPM, "S" is the stroke length in inches, "n" is the rod-to-stroke ratio, and 2189 is a constant. A safe limit for "Z" is about 100,000
ft/s2, although this will cause ring flutter with 1/16" compression rings.
Why did Honda choose a lower rod ratio? Shorter rod allows for a lower hoodline, since the engine fits nice and neat inside a shallower engine bay. They don't use a crazy high redline either. They don't like having recalls for pistons going through cylinder walls.
The low rod ratio motor will fill better with the small ports and a big cam at lower to mid rpms. The low rod ratio motor will not fill well when you shorten the time between one rev to the next. It runs out of steam at high rpms BECAUSE OF THE LIMITATIoN OF THE PORT SIZE AND VALVE SEAT (especially if the valve seat angle was set for enhanced low lift flow).
The high rod ratio motor will fill better with small ports and a big cam at high rpms. It has no inertial or haul in the low to mid rpms to generate the energy for filling the cylinder at low rpms. At high rpms, the higher piston speed at the furthest point away from TDC will help fill the cylinder when the time for the intake stroke is briefer (say from 6500-8000 rpm).
This is why the powerband locations are where they are.
So your view of filling is very static and a snapshot of one space in time. If you look at filling at low, mid, and high rpm, each rod ratio fills more efficiently at different places.