I think the cutout on the back at the top of the spine is larger on the Gen3 to work with some weapons that are slightly different than STANAG spec like the SCAR 16. I had to modify my Gen2 mags to work with my SCAR so it wouldn’t push up on the bolt release.
M3s will work properly with the SA80 and original HK416s, which have a magwell that's a bit longer and tighter than a US spec AR. The front over-insertion stop on the M3 is a bit lower and has an additional one on the back. The current HK416A5 and MR223A3 have the slanted magwell like an AR, but I'm not sure if they're still tighter. The US civilian market gets neither, so the MR556A1 still requires M3s over M2s. I've heard of some non-standard lowers like billet or those configured with magwell grips not taking M3s because of the stops, but that's not an issue for anyone not using weird stuff.
The M3 also has a slightly slimmer floorplate, so they stack better pouches where they double up.