I think there is also the problem of the fact that TES, unlike Fallout, isn't a post apocalyptic world, where theres no real communication with the other side of the continent. Tamriel is ruled by an empire, or by Skyrim's case, two empires, and whats going on in Hammerfell isn't exactly unknown to the people of Morrowind.
On top of that, each game has directly been the cause of the next
-Jagar Tharn impersonating the emperor, and letting The Empire fall to [censored], in Arena is what caused the political situation of Daggerfall.
-The destruction of the Numidium in Daggerfall led to Dagoth-Ur needing to construct the Akulakan in Morrowind.
-The Nerevarine freeing the heart of Lorkhan in Morrowind is what weakened the barrier to allow Mehrunes Dagon to invade in Oblivion
-Martin Septim sacrificing himself to stop Mehrunes Dagon is what led to the entire political situation in Skyrim, both of which were the last two pieces needed for Alduin to return.
TES is one singular meta-plot, in a continent where news from side is easily available to those on the other. There really isn't any room for something ELSE, aka an Obsidian made game, to be going on in all this.
Fallout is different, since its neither one super-plot, nor are means communication readily available. Bethesda can sit on their east coast, and Obsidian can camp on their west coast, and outside of a few small name drops/references, they can go about their day without ever coming into contact with each other.
And, as I have pointed out in other threads, Bethesda appears to have actively tried to make their east coast not mess with the lore of the west or Midwest, even going so far as to have Ashur not move into the major cities of the rust belt, such as Cincinnati and Detroit, even though they are just as close, if not closer, then D.C. and Ronto are, just so they could avoid the MWBoS.
I doubt letting Obsidian make a Fallout game was a hard decision for them. Bethesda seems perfectly willing to admit that that stuff over in the west and Midwest really isn't "theirs", even though they own the series, since it was made by another company, and seem perfectly fine with letting the people from that company make another game in the area they created, while they sit on their east coast.