1. The access controls mean that any file sin the D/D/D folders (Downloads/Documents/Desktop) and subfolders are protected. It may extend to the user's current directory as well (where the D/D/D directories live).
2. The actual program that the system sees is a shell script, issued when an X11 app starts and it apparently secures on that.
3. Some users of other X11 programs reported success by starting them under the Terminal app and answering the "provide access" questions on authorizing that to have full disk access.
4. The simplest (and probably most secure) method, rather than adding access permissions, is to use terminal or the Finder app to make a new folder from the root - that is not under your own user name but at the same level as /Users and /Applications etc and copy all the files you need into that using Finder.