The Fierce Deity Mask is...weird. It allegedly has all the 'merits' of the other masks, which would mean Stone Mask's perception invisibility might be active? We don't actually get to see the other masks abilities really come through the Fierce Deity Mask much so that's always been a strange statement, for example Majora is not at all affected in the boss fight so at least it can still perceive Link if it's true.
Isaac's kinda got enhanced senses, having hints at where 'Reveal' can unveil things that are hidden, but not sure if it counters the same way if the Stone Mask stuff can be considered legitimate. Ivan's "Reveal" is a lot more solid as an answer here to clear up that vagueness.
Also the main BFR is a Djinn that just knocks the opponent far enough out of the battle they're no longer a threat in game, don't think that will work due to range. Iris could in theory BFR by just yeeting the opponent into space, but that's getting creative, the move's never been used that way.
Also the AP is a bit of a disaster here. An Earth-Sun distance is in the 8 FOE, while Isaac is at least 1 FOE, likely higher, but to a totally unknown degree. They start in-range so Isaac likely gets one-shot to most things at current rating.
So Stone Mask perception being possibly a part of the Fierce Deity makes it unclear if Isaac can even fight properly, and the AP difference is pretty massive due to the lack of clearer feats for Isaac and the Golden Sun itself even if he can. And unequalizing speed is an absolute no-go because yikes on that blitz.
Fierce Deity, but to a level that feels mismatchy. If Stone Mask isn't valid, and Isaac's scaling chain with the Golden Sun is high enough that he's not one-shot, maybe we can have a hax debate, but otherwise this feels like Isaac has no options currently.