While in theory a through axle should tighten in precisely the same position every time, in my experience it is not always the case. It is damn close, and usually close enough for disc alignment, but not always.

What I have always done for wheels that sometime give me grief, is do the final tightening with the bike on the ground with a little bit of weight on it. Just enough that if there is some wiggle room, the axle will settle in to the deepest part. It just helps with consistency.

It also makes a difference what brakes you are using.... more specifically, the pad clearance.