How do you know that your stem is true with your flywheel when you use it (with paintbrush) for balancing?
I always turn the flywheel and the stem together, on the lathe, so I know that they are precisely concentric and aligned. I don't have problems of this kind. I use only stable and well seasoned wood for my tops, and I varnish it with epoxy resin, which is an excellent barrier against humidity, to assure dimensional stability. Also, it never happend to me that one of my stems becomes distorted or broken because of a too hard spin, (and I can spin quite hard), even when the stem is long, narrow and made of a very light wood like obeche.
In brief, I don't have this problem.
Some times I still check it anyway;
first I balance the top as usual, using the paintbrush on the upper part of the stem;
the result is that the balanced top will spin with the stem perfectly steady, no wobbling at all in the stem, at least at the height where the stem receives the marks of the brush.
At this point I observe the outline of the flywheel of the top while it is spinning, with a 20x lens;
the littlest wobbling of the flywheel will be easily noticed.
If the flywheel spins smoothly without any wobbling, as the stem does, it is ok.
If there is some wobbling of the flywheel, in
vertical direction, it means that the stem is distorted.
If there is some wobbling of the flywheel, in
horizontal direction, it means that the tip is off centered.