Gens and 2xsai

2xsai is great, but there's one downside depending on the game- for games that have black borders you can't use the stretch to full screen (shift f2) option. Is is possible for this to be fixed in future versions or is it a limitation of 2xsai? Also, why do these games have black borders? Are they run in 256x256? (examples are shining force1 and 2, and street fighter2 ce)