It doesn't appear to be an issue in desktop backup because we're simply restoring the contents of the backup, we're not referring to a defined list of directories and files. I can see this being a problem for tape.
Can the restore process not refer to some config db within the restore itself for that user-extensible list?
No - that's the chicken and egg issue. We restore the config dbs from tape/desktop backup, so we may lose the config values you need.
And if we did read them out of the backup, we'd need to read the backup twice, which we can't do as we read it as a stream. To read it twice, we'd need to copy it to the server before restoring, which would further limit the size of the backup file.
There is also a security issue of an extensible restore list. We intentionally do not restore any directories which might contain executable code.
I think one of the options I outlined will provide what you need. Have a look at the MySQL db dump/restore as an example. We dump a text copy of the db so that we can restore it later.