I've played through this 4 times. I even tried to send Dogmeat home before I went into the fort. It's always the same, whether I part ways with valentine at the end or not. Dogmeat is gone. I've searched the entire surrounding area and waited for multiple days. I've tried starting the quest without Dogmeat as a companion.
On the third playthrough vats locked into Dogmeat under the ground but I couldn't communicate with him.

I'm posting this both as a warning to other players to save before you begin this quest and because Bethesda doesn't seem to have a way to request support or to report bugs.
If Bethesda reads this please fix it. I'm very fond of Dogmeat and I'd like to finish that quest.