Since I was highly dubious about Phyllis' mental state, I convinced her (through persuasion checks) that she could make a fresh start elsewhere.

To me, that suggested she was leaving.

But so far, she has not.

Each time I speak to her, she just says either she's thinking about what you talked about (the persuasion check) or is just snarky.

Why doesn't she leave the Marina?

My conversation went a little different. It ended up with her turning hostile. She then ran outside, stepped on a land mine and died. I then got a message saying I could use the workshop.

That is some prime real estate.