I doubt that Bethesda would kill off the BOS in a canon ending - they might have to redo the cover art!

The Chosen One didn't stomp out the NCR or the BoS. I dont think the Railroad ending is the good one. The institute and Brotherhood endings are game breakers. My reasoning for this is as follows. There's not been an answer on a canon ending. No fallout has ever had the "bad" ending be canon: The Vault Dweller didn't side with the master. The Lone Wanderer didn't use the Modified FEV. I have some news for you: The BOS in Fallout 3 - 4 is a not mention worthy BOS outpost (and also traitors / outcasts to the real BOS). However if one was announced I think the either one of the Minutemen or the Railroad ending would be canon.