I don't see how it's any different to Civ, two civilisations with a joint agenda but separately controlled, time passes at the same rate for both civilisations.
So Xcom 2x bases, both with a joint agenda to protect the earth but controlled separately, so as described as objectives, each player can attack a UFO and play apart the client (as we all no it'll be p2p) just reports back the result of the mission, losses/kills etc when the mission is over.
I assume your complaint is over the time elapsed in the base/geoscape? In the original the clock stopped in mission which would mean the times between players would get out of sync? that's a simple case of the client/server recording the geoscape time when the mission starts, the server/client can then query the other party to see who is further on in time at the end of the mission and bringing them up to that date, increasing their research/etc accordingly sure it's not perfect, but if time in the geoscape is set as a constant ie 5min intervals it's not really going to hurt anyone.
The technical aspects are not the problem. Yes, my complaint is about the real time elapsed during base/geoscape. And everything that is dependent on that part of the game. People would just keep getting out of sync with the time-line. Facilities would get built, other events would happen.
You think setting the geoscape to 5min intervals would fix this? That's pretty naive. Since there is no way of knowing how long it would take for player 2 to finish his objective. Either you would have player 1 sitting around doing nothing for possibly 15+ minutes or the whole game progression would get messed up.
Progression is directly related to what happens on the geoscape scale (base building research etc.) If a player is viewing the base, normally time will stop. Will it stop for both players? Even though the other is not viewing the base? etc. Having a macro and a micro level and different time scales for each, just poses too many problems for a multiplayer game gameplay-wise.
You admit yourself that your sollution isn't perfect. A game needs to have a good flow though, I don't know how you can justify a half-assed sollution for a game release... a mod sure, but not an official release.
The only reason Civ works with multiplayer is because there are only turns and not a "real time" component. Every player begins their turn at the same time and "technically" ends their turn at the same time (the game waits for all players to finish their turns). Also game progression is more emergent in Civ while the state of the game is influenced in a more profound way by player actions in XCom.