If you don't mind it not running on console any longer, or on more accurate emulators like MAME and Cen64, sure. Might as well just branch over the whole algo while you're at it.
Project64 (and its derivatives) and Mupen use a rom database file to apply per-game emulation hacks to titles. With PJ64 (and likely anything based off it) open the .rdb, find the entry for the unmodified game, copy it, then paste it at the end with new checksum. The checksum is within braces like so:
[A4A9E67A-7A6FD9EF-C:45]Change the first two words to match the 8 bytes at 0x10 in ROM. The "C" value is the region code; you shouldn't need to fiddle with it but it matches the byte at 0x3E.
Mupen works somewhat differently; think it uses md5s for the entire rom, and you'd really be better off looking up how its entries are set up.
That said, all three sets of games have graphics plugin issues. They generate pokemon icons from the first frame or two of the animations, rendered and snapshotted from a buffer. Some that simply doesn't work, others that crashes after the first 2-3 times it does it, others can't apply the image right. Might need to use Angrylion.
"Anti-cheat" stuff enforced movesets and move counts. A move would appear red if obviously hacked (like Pincer with Megahorn or Houhou with Sky Attack).