I saw there was an update for the patcher;
"1. Updated readme to include more detailed patching instructions. 2. Updated xdelta3 command line in batch file to still try to patch a source file with a different CRC32 value."
This is IMO, bad. It's only going to cause you and others headaches down the line when people start patching the game to "bad dumps" and things break. CRC32 should be a lock in, I think the issue is the patcher looks specifically for the exact file name ie. "Ultima - Exodus (U)[!].nes", so if their ROM is called "Ultima - Exodus.nes" or "Ultima Exodus.nes" but have correct CRC32's, it won't patch. I would change it to look for the correct CRC32 or else fail, but file names shouldn't matter, like "123.nes"
My two cents.