If Danse hates the player in these circumstances why does he trade with them? He shouldn't be accessible at all. The partial accessibility is very confusing.

People aren't confused about Danse's motivations, people are confused because Danse doesn't tell them what he thinks about their choices which would allow them to understand what he's doing. I can think of a few ways to tie up the ending with him. Dialogue, a message, etc that would leave the player with closure (player knows why he's gone; because he should leave not become a container) instead of leaving the player to wonder if he's bugged or glitched.

I think Danse may also be holding onto the faint hope that, maybe, he'll be able to rejoin The Brotherhood at some point. Maybe once the Institute is destroyed, Maxson may look more kindly on him as less of a threat, or that maybe if he helps in The Institutes/Railroad's destruction, that'll somehow earn him recompense. Even if its a fools hope, its still something he can cling to.

Killing Maxson and wiping out The Brotherhood crumbles any sense of that permanently. Now he'll never have a chance at rejoining, because the remaining Brotherhood, if anything, will only despise Synths more.

Or open up the chance for him to rejoin. Pretending to be the last survivor from the Commonwealth, reporting what happens to the BoS.

Provided that no witness survive. Time to purge the BoS for Danse to rejoin.

I'm pretty sure that's in case you gave him your fully customized legendary instigating sniper rifle and forgot about it until after you blew up the Prydwen...

There's nothing to fix here. Many of the companions that have a quest tied to them won't reach maximum affinity until completing their quest. Nick doesn't reach maximum affinity until after Long Time Coming is completed, for Curie it's Emergent Behavior, for Cait it's Benign Intervention, for MacCready it's Long Road Ahead. For Danse it's Blind Betrayal. I wish this was the case for more of the companions. I was really hoping that they'd all have real companion quests.

For what it's worth, there are some Jewish Nazis in the world, as odd as that may sound.

Danse breathes Brotherhood. It's what gave his life meaning. He's ashamed of his discovery and ashamed at being booted from the Brotherhood. He still believes in their cause 100% though, and I think it's totally acceptable to have Danse alienate you if you destroy the one thing that gave his life meaning.

If your boyfriend is a Nazi and later discovers that he has Jewish heritage, he's not likely to stop being a Nazi. I present to you Craig Cobb - An American White Supremacist leader and all around horrible person who believes that the US should be for white people first. A few years ago he discovered that his genetic ancestry is 14% sub-Saharan African. He hasn't stopped being a racist yet. https://en.wikipedia.org/wiki/Craig_Cobb