They could have had a deal a while back, it depends on when this project started. If it was still in early talks with lucas arts, then who knows. The announcement was super early. Honestly until we know where they are in development it's hard to nail down.
It could be part of the whole deal with MS, or it could have been a prior deal bethesda had going on before negotiations even started. Who knows.
My point is now, starwars brand wise and gaming is way larger than it ever was in the 70's-80's. Even early games on super nintendo and Playstation pale in comparison to the sales of battlefront, jedi fallen order titles. Also seems EA still has a contract for starwars. So indy is free it seems, I do wonder since Indy has a connection to xbox from previous games, if this was something bethesda and xbox worked on together which maybe sealed the deal for their buyout.