Anyone know anything about disc brakes?

If you don't as you do the final 'tighten' of the quick release by closing the lever it seems (for me) to slightly skew the wheel/rotor from where you lined it up to. I tend to tighten most of the way with rotor aligned by eye, then hold the brake on and while still holding the brake lever close the qr lever. This seems to stop the wheel twisting and gets you a (hopefully) nicely aligned wheel and rotor. Sometimes takes a couple of goes. I imagine this is why thru axle is popular/may take over as (as I understand it) it solves these axle alignment issues.

Nope
Should I be doing that

I would say not.

If the calliper alignment is set up with the wheel/axle fully seated in the dropouts and the skewer correctly tightened/closed* then there should be no need to hold the brake nor to make any adjustments following the removal and refitting of the wheel.

*I have made the mistake myself of doing inital setup with the wheel poorly installed then wondering why the brake is rubbing after a wheel removal/reinstall.

Is it purely removing and refitting the wheel that's throwing things out or have you been taking wheel off to transport in the car then reinstalling and having issues? Ie, could calliper be being bumped or lever applied while the wheel is out?

Do you use a pad spacer when the wheel is off? I could see it being plausible that the change from being upright (in the shed, while riding etc) to laying flat (in the back of the car) could cause pad movement without the lever or calliper being bumped. Storing upside down or vertically can certainly have an adverse effect on hydros.

Could your axle be bent? If it were and you were setting the brake up with the bend in one orientation and then removing the wheel and refitting with the bend in another orientation could (I would imagine) potentially throw the calliper alignment off.