I would assume that as long as the mask doesn’t hinder FilmLabs ability to discern frames and sprockets etc that help it know its a piece of film it should work.
I was wondering same, since many of the films I use curl badly end to end (like Rollei CR200) or side to side (like Kodak Gold) and holding them flat is a scanning nightmare.
For my “desktop” scanner, I use its built in masks as well as the masks from an older film scanner that I’ve shaved down nubs that were meant for the other scanner. I also use a Lomography mask for doing sprockets in the scans. I hope to be able to use these with FL myself.
But I’ve make my own masks before using poster board with the edges cut just outside the frames and just laid it down on the film before too. This works for the phone camera and scanner app on the computer, so I don’t see why FL wouldn’t also work with them.