Really interesting observation.
I've never thought about that torsion bar in/out making a big difference to alignment, other than with it out on track you'll have more negative camber because you've made the front softer.
It must be the bars that connect the bar to the chassis that are ~1mm out so when you put in on they have to twist. I have no idea if that's a common occurrence or not.
The static settings are still accurate you just have to remember to re-do the alignment after taking the torsion bar out or putting it in. When you have the bar in you will have a bit of tension in some direction and probably opposite on either side.
You might also want to (if you can with your lasers) put the kart on flat ground and sit in the kart and see how the alignment changes, just keep the steering in the same settings (you can move it a bit to get back to the same toe on both sides). It's possible that it will already move towards more standard settings(if torsion bar put them off) because it'll be twisting back to normal... then you can account for this when setting the static on-the-stand settings.
imo front end toe/camber settings aren't super critical as long as you have them about there - caster and ackerman for example effect handling a lot more.