I've completed Human Error by allowing the doctor to kill the synth and returned to Covenant. The mayor there says something about being made aware of the arrangement and I can now use the workbench there (so it becomes just like any other settlement I've set up). Any further attempts to talk to the mayor just bring up a conversation about not trusting honest dan (with no triangle answer, clicking triangle has no effect and I'm only able to pick one of the other 3 buttons. No matter what one I choose further talks with the mayor just go back to the honest dan talk)

I've went to the bunker without honest dan and completed the quest, went back the mayor and got the "dont trust dan" talk. No way to skip it.

I've taken dan with me to the bunker and had him attack me after choosing to kill the synth, again the mayor just does his talk about not trusting dan.

Now heres the problem: Sometimes I will get a mission from the minutement radio station about a mission in Covenant or the town will come under attack and I need to rush over there to defend them. Problem is whenever I complete the mission (of successfully defend the place) I have go talk to the mayor to turn it in. Problem is even then he still only does the honest dan talk, I've tried waiting in Covenant or just standing in front of him to force him to talk to me but that hasn't worked. When I fast travel away the mission fails. Does this mean I'm going to lose named settlers from Covenant due to failing a mission for them?

Why do you need to talk to the mayor? Its just a settlement and he is just another settler now with some unique dialogue. Ignore him, stick up a beacon and treat it like any other settlement. He won't necessarily be the person you need to turn the mission in to. Have you tried everybody else?

He's the one with the icon above his head whenever I have to do a mission there. Just get normal conversation topics from the rest of the townsfolk. Have not set up a beacon there yet.