I've been keeping project files together, outside of the project folders. To switch to something else, I can double click the relevant project file without having to do much navigation in the file manager. To access the contents of the project folder with the file manager or terminal, I use a keybinding with geany/geany-plugins#1126.
Just to be clear, this pull request just changes the defaults for the option "General->Miscellaneous->Store project file inside the project base directory" and your use case is still preserved.