You open the parent project directory, right? That's how the file access controls work in MacOS. Sandboxed apps can't read files outside their sandbox until the user opens the directory/file in the file picker at least once. (Or something similar, I can't seem to find a source on that...)

I’d imagine once you open a directory you can open files within it (and child dirs)

Drag and drop project folder. Also, yes, I do open project directories using PyCharm's (poor) file picker.