I think you already know one way. If there is no crush sleeve, you cannot get enough force on your bolt to retain the wheel radially on an undersized shaft if it is not perfectly balanced. Even if you do have a crush sleeve, I think it is ill advised to use an undersized shaft. In my case with the all-thread, there were compounding factors. I used a through hole to mount the all-thread to the tool arm instead of threading it, I did not have a solid spacer from the tool arm and used a nyloc nut instead, and the all-thread was not exactly straight. The net effect was that the grinder was threatening to shake itself apart at even a moderate speed. What can I say, I wanted to test the wheel that day and that's all I had around. After the proper hardware arrived and I mounted the wheel properly, I was able to run at full speed.
The OP said the wobble is more prominent when the grinder is running, which is also what I observed with my poor mounting. I would say that if the run-out or wobble is amplified by the machine running, it is likely that something is happening at the mounting point. I cannot really see the wheel or tool arm deforming much, and the extra motion has to come from somewhere.