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.
I found myself in a similar situation recently. I found that within the MPR tool in the tools menu there is an option to “Remove marketplace metadata from module”. Using that tool, I was successfully able to remove the module from the marketplace modules section to the manually created modules section in the App Explorer.
I managed to do this in version 9.18.7 of Studio Pro by exporting the appstore module from the project, unpacking the project.mpr file, opening it in mpr tool and changing the FromAppStore flag, it was editable in my case.
There is also an option in this version of the mpr tool to remove all Marketplace meta data (in the menu under tools).
After that, reinsert the project.mpr file into the module .mpk file and import the file once again into the project replacing the existing module, in my case the module was now showing up as a local module.