It's been I while since I looked at this (the conversation was from 2020) but what I remember is that there were two ways to avoid the Windows warnings as an app distributor:
1. Buy a signing certificate for many $100s/year. (Something like that.) And some additional fee for Apple apps.
2. Have your program downloaded and ran by many people. I don't know what is "many". However, new versions count as a new program. So this makes development difficult.
I can't help what the user choses to do on their computer. I suspect that an educational program like ours (as opposed to a game, perhaps) would have a VERY small number of people willing to click past the warnings, or to have their computer set up some way to avoid these warnings.
However, our program works pretty well as an HTML5 app. The Progressive Web App essentially lets you sandbox your app inside the user's browser. So, we're trading some performance for user safety (or at least perceived user safety). But the PWA is installable! So it really is a good solution for us.
Speaking of which, I'd really appreciate feedback on the app!
https://www.ivoyager.dev/app/planetarium.html (desktop only for now)