I have always been surprised hearing people talk about thumb pain and getting callouses on the thumb. I have never experienced any of that, but I can't say why.
One thing that was an issue on my very first accordion, an HA-114B, was the plastic thumbstrap was uncomfortable. The problem was that the edge of the plastic was rather sharp, and cut into the skin a bit. But I soon replaced it with a softer leather strap, and that was the end of that problem.
Are people experiencing pain because the thumb strap is too tight? I hate an excessively loose strap, but I don't crank it down either. I find that I do like to use a rubber band, but again, it is adjusted to be comfortably snug but not overly tight.
The right position should help you (i.e. 45%, etc.).
By the way, you never have use the #1 top button. This is a redondant note that in the past would be used as a frame of reference to tune the accordion. #2 button is much easier to reach.