I can't speak for everybody who uses acme style pins, but I make mine for alignment. V-groove threads always seemed to have inconsistencies for me, with the pin resting on the softer side of the wood, which is not dead nuts center. Of course it was never anything severe, but enough that I wanted to have a pin with a straight & consistent barrel that would fit flush & smooth into the shaft's bore. The threads do nothing but hold it in place. With v-groove threads we have to depend on the threads to do everything, align AND lock. Again, nothing wrong with v-groove threads. They just are not accurate enough for what I want, so I make my own flat bottom thread pins.
As for phenolic big pin joints vs. stell collared small pin joints, I think there is enough difference to feel. I generally build big pin flat faced joints, but at times do the steel jointed 5/16-14. Everything else the same in the consistency of my cues, I can tell a difference in the hit & feel. Anything different in the cue will give a different feel, a different sound, a different reaction to impacting the CB. The differences might be subtle or might be vivid, but it doesn't take a genius to know that there will be a difference in performance based on material & build style. Some players may not ever be in tuned enough to feel the differences & some players know it right away. That's why everybody has differing opinions. But mechanically & physically speaking, there will be a difference between a big pin phenolic collared joint & small pin steel collared joint. They will resonate differently, giving a different feel (feedback), they will sound different, they will have differing effects on the overall stiffness of the jointed area of the cue, and because of the other reasons they will cause different playability characteristics, even if subtle. It shouldn't take a machine to figure that one out. That's just common knowledge of the different materials' mechanical properties & vague knowledge of physics.
The major difference comes in to play when there are so many different builders using their own techniques & chiming in like they are vastly experienced in all of the joint systems. Reality is we all have our favorite joints & our experience is biased toward what we favor, and understandably so. To actually test any of this, a builder would have to make a universal joint on one cue & shaft that can be changed from one joint type to the other without changing anything else on the cue. I don't particularly care to do it, and know no other builders who would really want to waste time doing it. The projected results can be argued all day but none of can prove anything until this cue is built. So it'll remain a debate likely forever. We'll all still use what we favor, anyway.