New industry acronym: b2h (butt to hand)Butt to hand measurements are similar going from 1st to 2nd gen Megatrail, and as above, similar from 2nd gen Medium to 3rd gen Size 3 (short). You could just prefer the bike a little shorter, or when the seat tube angle got steeper for 2nd gen, that could explain the difference (1st gen gets proportionally longer in cockpit as the seat gets higher).
50/60mm stem length recommendations are baselines to get folks as comfortable as possible. I wouldn't read too much into them, it's a baseline gathered from feedback over time. As far as weight balancing, yes, that's part of it, but to really dial that in, has to be done on a rider specific basis. I've done front/rear weight balance measurements, and leaning forward/back even just a little bit changes the weight balance at least as much as 10mm of stem length. It can easily change the balance from 60/40 to 55/45, for example.