Don't credit us with too much - I can't do the maths anymore, I was never any good with experients & I was ony theorizing. Even so, I think the answer is "yes"
Basically, I think the interesting bit in a lot of this concerns overlap &/or when valves are open when the piston is going in the wrong direction. Despite the fact that the most bog-standard engines imagineable make use of that I find very difficult to get a feel for how big the effects must be. The effects include the exhaust flow sucking the inlet flow after it; scavenging; once a flow has some momentum then it'll carry on going until some other force stops it; turbulence getting good mixing & keeping detonation at bay; venturis; changing densities; stand-off, flames coming out the exhaust etc etc etc. Which are the big effects & which are the small ones is what baffles all of us.
Re. small ports & high velocities, I'm an agnostic. In it's favour, first I'd cite Cosworth. Remember the famous story of when they went to Indy in the '60s, saw some Offy heads & quipped that they should have arrows in them to tell the gas which way to go? Sounds to me like they were small(ish) port men. A second reason in favour would be sizing Weber chokes - we all know they can be too big for their own good. Conversely, I once saw a real cutaway Renault F1 engine & the ports didn't look that small to me (******* huge would be a better description). I also can't see that high velocity on it's own explains a lot. If you want to maximize momentum (M*V) then more flow (Cubic Feet per Min) does that if you keep time constant.
Couple or 4 thougts on that mototuneusa site. I couldn't find his explanation for his D-shaped ports at all - my guess is it's to do with scavenging between exhaust & inlet and/or maximizung the flow round the unshrouded sides of the valves. Second, bikes are pretty low-tech compared to F1 (much less time & money). Third, he's done quite a lot on bhp-restricted stuff - hence the benefit is all in terms of wider power bands (useful in rally/hillclimb applications?). Fourth, bikes & riders have problems handling ginormous horepower at the best of times - he himself says smooth delivery matters (& it does to me too).
It's just a great big fog to me. Anyway, must stop warbling & see what trouble I've got into elsewhere.