2) why the lower ammo of the electromagnetic rifle (from 8 to 2)? I realize it's now more of a step up sniper rifle than in previous versions.
They are an extraordinarily accurate and powerful weapon for the early game, so they have high TU costs (that includes reloads). There's also a "story" reason. In order to stay accurate, the rails along which the projectile are shot must be replaced after every shot or every other shot or something like that. Can't remember, but the point is you can't pack a lot of shots into the reload. I may have gone overboard with the TU costs a bit, but I'll revisit it at some point.
3) How are the Alien gas grenades produced? I seem to get them from missions but are they automatically produced at a certain rate & appear at my bases or are they recovered items from missions? They seem to available at start.
I think the aliens begin using them from the start of the game. They are items recovered from missions.