However, using external devices to pry into the code while not technically manipulating the game through unauthorized means, does involve you getting unauthorized access to info you were not mean to see.
I don't think this is actually relevant to whether or not RNG manipulation is fair (it could be fully legitimate to access this information, but unfair to manipulate it through ways that the game developer clearly did not intend; fairness and legality are not the same thing) but at the heart of this question is the issue of whether or not you own the code to the game you purchase. After all, if you do, then the very concept of access to it being "unauthorized" is nonsensical. However, that's a more complicated question than you might initially think. On one hand, decompiling, manipulating, or otherwise modifying the code of a game you own is legally perfectly fine, so long as you don't redistribute it. However, if you
do redistribute it, it's piracy.
A lot of companies don't want you modifying their games. Rockstar, the developers of the Grand Theft Auto series, are particularly notorious for this, and go through not inconsiderable lengths to make their games as difficult to modify as possible, and shut down modding projects they don't approve of. However, they don't really have a legal precedent here to say that decompiling their source code shouldn't be allowed, which they would need for accessing their game's source code to be considered "unauthorized". Basically, there's no legal precedent for companies being able to tell you that you're not allowed to examine the source code of a game you own, so I think calling it unauthorized is a bit misleading. However, the whole subject is a bit of a legal quagmire where there isn't a whole lot of precedent for
anything, and it's undeniable that the publisher owns the creative rights to the code if nothing else. It's a question of whether or not that is enough to say that the end user shouldn't be able to examine it.
But again, none of that is really relevant to the question of whether or not RNG manipulation is fair, and the answer is pretty obviously no, at least in the most literal sense. If you take one player who used RNG manipulation to perfect his team and another player who didn't do that (I presume we're talking in the contexts of before Gen 4, when breeding wasn't a viable alternative to RNG abuse), the player who manipped has a significant and undeniable advantage over the other player. That being said, for better or worse RNG manipulation was considered the standard back then, so not doing it would be paramount to putting yourself at a disadvantage.
In a way you could consider it like EV training. It's debatable whether or not GameFreak truly intended for players to min/max their EVs the you do in competitive play, or if they simply wanted to encourage battling against other Pokemon to get higher stats instead of stuffing your Pokemon full of rare candies. A player who EV trains his Pokemon has a significant advantage over one who doesn't, but
not EV training out of some misguided sense of honor or belief that EV training isn't how GameFreak intended the game to be played would itself be kind of a silly thing to do. RNG abuse is similar, but taken to the next level.