This is a well known problem in diy cnc. A work around that does not involve modifying the machine is by making your own waste board or just an additional kind of platform on the SM waste board.
So basically you place a plate on the machine and flat mill it completely. So now you have a work platform that is for sure parallel to the XY axis.
This method is almost a must if you want to do double sided cnc. It is a bit of initial setup but I believe it will save you tons of pain later…