Rolling machines use flakes, rather than shreds. If you look at the YouTube video of FX Smith's Sons rolling machinery in action here:
https://www.youtube.com/channel/UC1Nh_bRHgFFIvaAHVrAxrrw
for example, you will see flakes in the hopper. There are none of the scriggly pigtails that get chopped off the ends of filler, no stems... just flakes from de-stemmed leaves. These flakes probably average two to three inches across.
Have you tried removing end bits then cutting your scraps into flakes?
The Cuban sandwich, as I understand it, spreads these scraps onto an intact half leaf before binding. Have you tried that?
My solution is simply to do everything possible to avoid making waste. That's harder to do with a parejo than it is with a perfecto. A perfecto fits the natural shape of a leaf. Have you tried making perfectos?