The lowers/stocks should have no effect on the functionality of the uppers, as long as they're in spec.
Rifle length is a gentler system, since the gas travels further before expanding all the way up into the BCG, so it does more "Pushing" the action open, rather than "popping" it open.
The pig-tail will help that on a much shorter barrel, but on a 16", it's may not have enough power to cycle the action. You may have to enlarge the gas hole in the barrel to get it to work properly.
My advice would be to either buy a true mid-length system and stick with it, or buy a true CAR length system and stick with it. Both of them work, and are reliable, out of the gate. If you go changing things up, you're more likely to run into bumps in the road.
If you're like me though, you might enjoy the challenge, and the learning experience you'll get from it.