So apparently my theory on Flange Focal Distance being a factor in my focusing problems seemed to be a dud. It turns out that I can hold the camera actually a fair distance away from the flange mount without any observable degradation in image quality.
In hindsight this makes some kind of sense. As the microscope acts as the camera’s lens, the light hitting the sensor must be relatively parallel.
To test this I actually decoupled the camera from it’s mount and shot lens-less from a ways back in a darkened room.
So going from fully attached to several dozen millimeters out changed my image impressively little.