Your last point is a good one - the cracking could lead to increased run out.
This site suggests manuf tolerances are typically around 15/1000th inch - or 0.38mm. Deformation of upto around 0.6mm is not visible to the eye.
Irrespective of the tolerances, I'm not convinced a deformation of such a small amount (e.g the 1mm reported above) that that is being observed above should result in a crack - unless the material properties of the alu alloy are somehow unusually brittle, or contain flaws which precipitate stress raisers and hence cracks during "normal" loads - both of which would suggest a manufacturing defect problem.
Good luck with this. The fact this issue is common suggest these wheels are not fit for purpose. The fact that all 4 wheels are out suggest the forces being experienced are far from abnormal in use, hence not fit for purpose!?