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