Topgun's got it - For AR's, you're more prone to be limited by mag length than chamber length, so you gotta find a load that works for you that's seated as long as they can be and still fit in the box. You mentioned it in your opening post, so I didn't elaborate on it, but it's a fact of life - rounds gotta feed right, not just shoot straight.
AR's are notorious for short mags, but it's somewhat true for lots of repeater action types. Bolt guns tend to have luxuriously long mag boxes, but even some bolt guns are vulnerable. Weatherby's have massively long leade's to allow such great pressures and velocities, so as some of the other guys mentioned on another thread recently, even bolt action weatherby's get limited by the mag box. I personally do a lot of levergun shooting, where the COAL across the carrier becomes pretty critical for reliable feeding. Some tube type bolt guns might have ejection ports too small for max length COAL's. I used to shoot a benchrest load that if I didn't fire it, I had to remove the bolt to eject the rounds. Hit the wrong COAL with the wrong bullet, a round can skip off the feed ramp and catch the top of the chamber (pops over the mag lips too early)...
Just part of the great number of things that make you wanna pull your hair out after you find your load and length that gives optimal accuracy.