Did you not read the itch.io page for this game? They have stated clearly that this version on itch.io is going to stay the 2017 version and is not going to change or be updated. They have moved to Steam and are keeping this version for both posterity and as a free demo of sorts:
"Welcome to the Autonauts Prototype! We haven't updated it since the end of 2017 and have no plans to do anything else with it, but here it remains for posterity (or a crude introduction to what the game's about).
If you're interested in more, click the image below to be taken to the full release on Steam!
PUBLIC SERVICE ANNOUNCEMENT
Please don't post about the Steam version here, not when there's such a lovely space to do that in the Autonauts Steam Community. This itch.io space is dedicated to the prototype only. Cheers!"
Not sure what issues you have, some of that sounds a bit too extreme to say it's 100% Steam or Teams if you're having to reinstall your os that many times. Either you're setting or doing something wrong that they don't like, you got some driver issues, or you got some hardware issues. But, with that many installs, it's less likely the latter two. Either way, good luck, hope you find a way to figure out what the issues are and fix them.