That's a tricky situation. As far as I'm concerned, Google should allow the "drive.file" scope to access the current document, regardless of whether it's picked or not, IF the user has approved the "currentOnly" scope.
But, that's not the case.
The only thing that I can think of, is to prompt the user to pick the current document when they first open it up, or set it up, or open a sidebar. Something like that. You'd need to explain to them, that it's got to be done. I don't know if you can add a filter to the picker to show just the current doc to make it easier for the user.
I've also thought about having the code create the file that the user is using first, because files created by the code are available, but usually people create or open their file first. They aren't going to want to use a new / different file.
I don't know if there is a good answer for this situation.