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Some notes first:
Pheromosa and Naganadel are unviable in the current metagame, especially the latter as it's entirely outclassed by Eternatus. Pheromosa is difficult to justify over Deoxys-A as it can't break past the common metagame staple that it can't even wear down known as Ho-Oh. More...
It was already stamped in the first place, as said before, so it'd be 2/2 after applying it, if you don't think you'd have to take a second look to corroborate, that is.
Statistically speaking no, especially when ignoring specific cases like RNG Manipulation (certain shiny + IV combos are only possible on certain TID + SID combos, more notably when not breeding), or the Cute Charm bug. The number of PIDs that are shiny are always the same per save file given how...