I've had a look around, and it seems as though the “FromAppStore” flag is baked into the module itself and cannot be changed from Mendix Studio Pro. The flag is visible in the MPR Tool but can't be changed there:
I think at this point the easiest way to get it into your normal modules is probably to copy all folders from the module into a new module in your project. It's ugly and a lot of work, but I don't really see any other way, unless you want to manually edit the .mpr file, which isn't really recommended.
Alternatively you can say “whatever” and just rename the module to “ModuleName_NotFromAppStore” and hope that conveys the message to your fellow developers.