I must point out that I am aware that wacky scifi has been a part of Fallout from the beginning, but I just feel like this DLC took it way too far. It's always been contained to some extent in the past. But still, plasma rifles, super mutants, and ghouls all have an explanation while the Courier's Brain did not. That's what really frustrated me.
Just think of it as a temporary and minor form of mental illness. Phantom pains are an odd phenomena that occurs when a person loses a body part, so it's not outrageous that someone could become mentally ill temporarily if they lose their mind.
For instance, let's accept the game's claim that it is possible to remove a person's brain and still allow it to remotely control the body via tesla coils in the skull. So technically, you're still "whole," just your brain is remotely controlling you.
However, from your (brain's) OWN perspective, it is indeed safer in a glass jar. You can stay there, live forever, be safe and still control your body, though we don't know if there's a specific distance where that stops working, nor does the Courier. There's that possibility that if the body dies, the brain lives on, so yes, remaining seems promising.
Still, the Courier is just as ignorant to the tech as you and I. He doesn't know how promising such a proposition is because he doesn't understand it. He just knows that brains are supposed to be in the body and that's how they naturally control the body. So from your perspective there, you need to get back in your body.
And that's where the conflict occurs: through the Courier being just as confused as we are, not knowing how it all works and what's the best choice. Thus, he begins arguing with himself and even percieves himself as hearing....himself.