Looked into it a bit more, and i feel kinda dumb now lol. The archived Renpy Repository did in fact seem to have PyInstaller, which was meant for a tool they were making called "RenPython", but I cant seem to find that tool inside of the current RenPy repository, or at least I cant find any file/folder labeled "RenPython". So I'll just assume that this tool was probably canned. Also, I didnt get flagged by Windows Defender. I think it was from MalwareBytes. If I tossed my game's exe file (not the game's zip file), it would get flagged by 4 out of 70 antiviruses as malicious, which one of them also happened to be MalwareBytes. And tbh this is expected since pyinstaller is pretty much known for getting lots of false flags for pygame projects. hell, I once had Norton delete a quick test build of an entry I made for last year's cozy autumn jam lmao.
So im gonna conclude that RenPy has probably developed its own method to distribute RenPy projects, and your situation of getting flagged is pretty different to mine. So uh yeah, sorry about bothering ya and I wish ya the best of luck on the results when the rating period ends!