It's possible that M2 did have Genesis Syndrome and it just didn't progress because time was frozen. The fact that she knows how to use Melia's archetype powers in the first place means she probably had experience. If Madame X is an alt universe or past version of Maria/Melia, her suit might have some type of system that prevents Genesis Syndrome from progressing. She could want Melia's light to get rid of it
I think the light plague thing is a reasonable possibility. Perhaps its a leftover effect of the Garufans being from the old world. I noticed that the fading thing that happened after the Garufans killed Arceus looked suspiciously similar to what happened to that one Xen Deathwing in a Neo Gearen sidequest. One reason Madame X wears her suit is probably to prevent the fading/light plague effects.
I've noticed that Leech Seed is also pretty effective against these bosses. Whimsicott makes a pretty good mon for the second fight with Leech Seed, Protect/Substitute, Grass Whistle, and Moonblast
spread moves are really useful here. i ended up powering through with my heat wave from ninetales and hyper voice from heliolisk. I noticed that the your mons get full hp/status restored between fights if they don't faint, so if you get down to one or two opponents you can pull out a bunch of revives.
Sludge wave is useful in this fight since it transforms the field and prevents Porygon Z and Clefable from getting stat boosts. Garbodor can learn it from the tm you got from Aya