Well what it mainly means is that you'll never be able to see all the OU Avengers assembling and fighting against OU Loki, because the Loki and Tony will never be able to interact. Judge for yourself whether it'll get in the way. Personally, I think it's problematic. Tbh, I don't see how what the mods have done is even a workaround, because it doesn't prevent the other Avengers from updating to the film, and surely if they did it would be IC for them to get in Loki's face anyway. Maybe that would be less of a problem for you if you were playing an AU character.

Personally, I'm not a fan of OU Loki's characterization. I can't judge on the Thor since I don't think he's as active as Loki. I would be interested in seeing an AU of either of them!