As a pathologist, I spend a fair chunk of every day using microscopy optics which are in every way equivalent to AR's IPD problem. The honest answer is your brain has to learn to integrate those two images, and it will take months of daily use for multiple hours, with associated headaches, neck aches, back pain, etc to figure it out exactly right, but the trick is that by then, you won't have figured it out exactly right. By the time everything snaps into place, you brain will have also learned to snap it into place. My eye-brain system gathers information through oculars in a way that others do not. It's a matter of physical training, like so many things.

That's not to say quality doesn't matter. My undergrad is in physics, and the quality of the oculars in a clinical microscope puts to shame pretty much everything else I've seen. Even telescopes at the tops of mountains aren't as nice, ergonomically.