Depending on the design you might also find that a long 'tail' of 120 or 135 film sticking out of the neg carrier gets in the way of the frame/mount/edges of the carrier (as it is made to have just the 4x5 neg between the glasses, in the middle).
I will be making a 135/120 carrier for a big 10x15cm Magnitarus for this same reason. Anything which fits between the glasses is fine, with masking, (currently 4x5" and individual 6x9cm) but the glasses are recessed in to the main part of the neg-carrier so nothing can 'stick out the side'. Not a problem when I eventually get some more 3mm plywood (famous last words).
Edit: Yes, you certainly should mask out the light that isn't going through the negative. The whole darkroom would light up!