Strange, I wouldn't be able to tell you what's triggering that. It seems that the false positives are only coming from companies using AI-powered detection. Other GameMaker developers have had this issue too, for some reason.
There were definitely plans to include many of the features you mentioned, including an upgrade system, but the scope was getting large and I'm still working towards a degree in an unrelated field 😵💫. I may revisit it one day!