Nice, good looking out. I figured they were for different cases you were speaking of. Do you use UGC cases for your SNES collection and the other bit cases for NES?
Either way I would have no issue buying/using the bit box cases for NES. I think it would look cool to separate them etc.
I started out getting UGCs for NES, SNES, N64, Sega Genesis and 32X. But over time I switched the Genesis and 32X to official Genesis and 32X cases, and then once Stone Age Gamer came out with their NES BitBoxes, I switched my small NES collection to those. So right now I only use UGCs for SNES and N64. But once they release their SNES and N64 BitBoxes, I'll likely switch over to those completely, and only use a handful of UGCs for any accessories or things that don't fit.
I like the NES BitBoxes a lot more - no modification needed, they are formed to fit any NES cartridge, and have an optional pouch to hold manuals. They are more expensive than UGCs, but I find the quality to be better overall. I also think they look nicer on my shelf, and generally look more professional, since they are designed for the NES carts.
Similarly, I started out housing my Game Boy games in EU DS cases, then switched to 3DS cases once it was discovered that they can hold them with no cutting, and just adding padding to hold it in place. Now, I'll be switching to ShadowFox's Game Boy cases, since they are specially designed to hold almost all Game Boy games, and match the DS cases. In both the case of NES in UGC and Game Boy in DS cases, I hated having to cut and modify them.
I'll look into updating some of the old covers I did where I left off the 1-2 players icon. For other peoples' covers, you might just throw it into the template with just that icon on and then save it.