There’s know way to know the inside of your managers head but from the way you describe them they sound very decent. I would like to think I’m a similar kind of manager and have definitely gone to bat for my people in similar ways - but I always make that they know I will support what’s best for them. I had a similarly valued employee leave under similar circumstances about 6 months ago. Because I’d always told them I’d support what is best for their career they felt comfortable coming to me to tell me about a new opportunity to pursue a PhD and I although I was sorry to lose them I was very very happy to see them advance, and also grateful that they had felt comfortable enough to tell me months ahead of time when they still weren’t sure.

Again I can’t say how your boss will react, but if it was me I would just be happy that you felt comfortable enough to tell me. Going to bat for you should not be something that implies you owe them. If that’s ultimately the way they see their own behavior “you owe me for that” then unfortunately you’re still probably better off leaving.

If you talk to them openly they also might be able to offer some solid positive insights from a longer experience.