1. When you are gassed, all your companions simply abandon you (the same thing happens in Raven Rock).
2.You somehow walk all the way back to the Abandoned BoS bunker, yet inexplicably and arbitrarily can't return.
3.How do you get rid of your collar, anyway?
4.You'd think Elijah would see the wisdom in letting you keep your gear (I understand it gameplay-wise, but still), increasing your chances of survival.
You have to realize that Elijah was a victim turned to would be conquer, mad man, Somewhat mad before, now total bonkers until you show up and turn the tables at the last minute using his greed for your need of escape.
Once you defeat Elijah, and there's more than one way to do so, the collar comes off. Upon your return it's explained why you can't go back, but may see her again