i finished the game siding with railroad, so i destroyed the institute. i never took x6-88 (or whatever his name is) as a companion while i was still friends with the institute. after destroying the institute i assumed x6-88 was gone (or at least hostile), so i thought i would never be able again to use him as a companion (and i didnt care much).

now i started to get all companion perks, and while doing that i found x6-88 somewhere in the wasteland (forgot where exactly, he was just standing there). i could interact and speak with him, including telling him to follow me as a companion. so i thought great, he is not lost after all and i can still get his perk by maxing out affection. since then i have him as companion, but he seems to be bugged. he never follows me, he just stands around and talks the same 2-3 sentences when i get near him. sometimes when i fast travel he pops up beside me, even fights if enemies are close, but he does not follow me when i walk away.

so, is he just bugged, or is the fact that i can still take him as companion after destroying the institute already the bug?

I heard that X6 will be available around Libertalia after Institute's destroyed.

But I haven't proved it myself in my own game.

Ive played all endings and like you didnt really use x6 much during the game but ive noticed he spawns either hostile or still available to use on a long cape heading towards Fort Strong pretty close to the dock near the Libertallia. Ive had your issue with all companions at some point or another. Its weird, i will go whole missions where companion disappears then jump in an elevator or fast travel and suddenly they will show up. At this point i dont use companions because i get much more carry weight without them. I never tried getting x6's perk. ive got all except his, Danse, and Deacons.

I've seen him out by the Libertalia a few times. I'll have to try using him as a companion now just to see what happens.

It's a bug, he's supposed to be hostile and killable after you destroy The Institute. Same thing happens sometimes with Deacon after you destroy The Railroad.