A few points:
There still seems to be friendly fire on your side of the battlefield. While archers and crossbowmen never seem to shoot their fellow unit members in the back, they still sometimes hit friendly units deployed in front of their own unit or standing mixed up with them in the same spot. Try sticking some spearmen into some crossbowmen: You will take a few casualties, if not as many as in Rome. So the trajectory of projectiles has to be followed by the CPU from the start.

As long as you have to plot the whole trajectory for the animations anyway (and yes, I can see arrows impacting quite clearly - I also have a rather high end machine here and all details on full. Unit size is large, btw, so there are a lot of arrows from my English Longbowmen in flight at most times), you can also put in the rather simple collision detection. It's simple math: The intersection of a curve with a plane. A complicated plane, in that it has holes where no people are, but still a plane. It wouldn't be too difficult to do a planar projection of every soldier on the field for the PC - it has to do that and much more for real time shadows anyway (if you turn them off, this doesn't compromise my argument: the mechanics are there).

The issue of enfilade fire that was raised makes it very clear to me that collision detection has to take place somewhere. I think it must have been there even as early as M:TW (dunno if Shogun had enfilade, never played it).

That the second unit didn't take any casualties in the musketeer test can have many reasons: At max range, accuracy decreases massively, and the power of the projectiles does, too. Many bullets were probably stopped by men in the first regiment fired upon, even if they didn't produce a kill because the sword unit was heavily armored. So I don't think there have to be some mechanics that don't let the bullets fly farther. Most people here will have experience of low-trajectory fire like bullets or crossbow bolts hitting two units in a row, and this can easily be confirmed by more tests, I'm sure.