Why would you preserve previous builds on the game page? Itch is a store front and not a code repository. If you want to do this, why not simply use a version number in the file name.
No, your newest exe flags as malware when scanned. No auto flagging it because it is unknown, it is heuristic positve. Many godot games have this problem, you can google it, and maybe ways of distribution to avoid that. Like a portable version inside a zip, instead of runtime package or whatever this is. It is very bad, because, how are we supposed to distinguish godot games from real malware inside a godot game?