I ended up with the Minuteman ending as I did join the Institute for a moment but after the battle for bunker hill quest I told Father I could not continue which led to me being kicked out of the Institute. The Railroad then told me they could no longer fight the institute as I was banished, and asked me to go to the minuteman for help.
So I go do the minuteman ending. Railroad is still up and running. The Brotherhood are annoyed that I saved the day with the minuteman instead of them but I'm still an active member and still capable of doing their post-game radiant quests.
The Railroad however are quite bugged. The dialogue from Desdemona assumes Glory was killed during the non existent Brotherhood assault on the Railroad, which never happened since I went with the minuteman before the railroad and brotherhood could go at it.
P.A.M also assumes the Brotherhood has been taken care of and that I destroyed the Prydwen, and sends me out to destroy leftover Brotherhood vertibirds even though I am still an active member of the Brotherhood, and that the Brotherhood is alive and well.
The Brotherhood work fine in the minuteman ending even though there is a big quest where one can destroy the brotherhood if they so please. (I believe this quest is only triggered if one is enemies with the Brotherhood, which I am not) The Railroad however seems to default into thinking that you went with the Railroad ending and assumes things that happened in their ending happened in the minuteman ending (such as the destruction of the brotherhood which costs Glory her life).
From the looks of it, The Railroad faction is just issuing the wrong post game dialogue and quests.