Sorry I'm going to the be the stickler here.
I don't get why you used a tool to do something where you could've done and created a verification movie instead.
If you call for sync issues when a memory card is placed well there's two NTSC-U revision differences and a single NTSC-J version they should be more than enough to help create a non-tweaked version.
Alternatively you could've gone with the bios route as there is enough of a difference which will allow it to have an advantage.
I'll show you with my favourite game example I usually have on hand, Tekken 3.
I know, Tekken 3 is not Mega Man X6, sorry. But I've done this test with various other PlayStation games in the past.
This file uses NTSC-J's two revisions and the NTSC-U version to select 3 different characters without changing the bios either (to be exact what I mean by this I meant between the NTSC-J versions since SCPH5500 and SCPH5501 are already different in that regard).
To tl;dr that file with a set of images:
Each version/revision was able to select a completely different character starting from Xiaoyu.
If you want to prove any of this wrong all you have to do is create two separate verification movies saves that unlock Zero and then create a movie that
fails to select both X in one version/revision and Zero in the other.