That's not an anti piracy check. A handful of snes games have special chips inside, like the FX chip for Starfox for example. In the case of Mega Man X3 (and X2), they have the CX4 chip. In order to make the injection work, you need a BASE game that emulates the CX4 chip. Luckily, both Mega Man X2 and X3 were officially released, so you can download them and use them as BASE for the injection. I did this with X3, where I used the official X3 as BASE and injected an X3 hack. Worked without issues.
Here's a list of games that use special chips so you can more or less guess what game to use as a BASE:
en.wikipedia.org/wiki/List_of_Super_NES_enhancement_chips