Couple things here, powder coat is not affected by oil or grease, but then I don’t see any reason to paint the axle in the first place. Just treat the shaft with phosphoric acid (Naval Jelly or Coca-Cola) and leave it bare.
I see what you are trying to do with the heat shrink so I don’t see any issues with heat or stress. I assume you will be using a piece about an inch or two long and it will be about half on the shaft only and the rest just covering the small end of the boot. Once it shrinks, it will clamp that end of the boot pretty good, I just never thought of using HST for this application.
Something else that would really clamp it down would be PEX tubing, but you would have to find the PEX in exactly the right diameter, then get the tool for expanding that size tubing which costs over $100 and you would have to work very quickly. Probably not an option, but manufacturers might look into this because for a high speed assembly line, it would be faster and cheaper than what they do now, but not a DYI for repairs.