not sure if its just me, but it feels like its a lot easier to get a design through the flow without specifying a core area, could this cause problems later down the line or is it fine as long as the user_proj_example and user_project_wrapper are always built together?

It's fine. You pretty much need to rebuild

user_project_wrapper

every time you build

user_proj_example

anyway.

That might not be the case if your design instantiate external gds