I have a couple of Wheels hangers, & I think that they are stiffer than what they were replacing.

If you're talking about 5-6 mm difference at the rim, that shouldn't affect shifting- I would guess that a third of bikes on the road

have that or worse.

I think you are splitting hairs- expecting a bit of cast aluminum to be true to thousandths, and assuming that the dropout/frame is perfect.

just use the tool- the hanger isn't going to break from minor adjustments- & go ride.