I have seen many people recommend this, but I have never seen issues of flare and I do not mask out the lightbox. To hold the film I use a negative carrier which has roughly 1.5 inches of black frame all around the aperture, and I use a lens hood on the macro, but that's it.
during my earlier experimentations, I had film holders which did not mask much around the picture. I experimented with various devices, cardboard, empty slide mounts (to hold the film flat), Lomography's Digitaliza, etc with various results. All light entering the lens around the image created flare. On top of that, handling was poor. I ended up recycling an enlarger's neg holder which has enough black frame around the image, and the issue is gone. I think that as long as no bright light enters the lens around your picture area, there won't be any problem.
I also switch off the room's lights so as to avoid reflections on the film.
I now manage to scan an entire roll in 5-15 minutes - the longest part being getting the neg out of the sleeves and back into them again.
Thanks for the comment on lens hood, I should use that too

(I just need to find one... don't have one yet)