Starsector 0.97a is out! (02/02/24); New blog post: Simulator Enhancements (03/13/24)
Hmm - what you're doing (fullscreen at a lower resolution) is indeed what I'd suggest.I think if you right-click on the game and go to Properties, on the Compatibility tab, changing some settings there may resolve the issue with it not actually going full-screen. In particular the stuff under "change high DPI settings" may be relevant.