logic of all rebalance changes doesnt work like this, they are always based in the best scenario any pokemon can give, for example best tms he can learn, best combo they can do, if after this is killing their weakness easy, then there is a problem that need to be solved, and this is the way how most of the changes you see are applied on game.Rhyperior is paper, BUT did you check his dmg? Not all pokes are made for duels, and one of them is rhyperior, this poke was made for exp, he overcompensate his low HP by his huge dmg.
2# Rock could always destroy fly/dragon.
No, this only give you advantage in types, in this way, why fight pokes cant beat e.g. porygon? They have type advantage and still loose.
As you said, salamance can destroy magcargo, main by rain dance, but not all players put this tm in poke, and magcargo is not poke for duel like rhyperior.
It's not pure rock, he have too fire type, so half of his skills are fire, so you could say too, that he can't beat meganium(?), but he have fire type.
And he can learn reflect and ss, so if you put them both, and fight against salamance with raind dance and maybe something price will be same.
There aren't pokemons that are exclusive for hunt or exclusive for PVP, after lot of changes done last months, all pokemons can do better in pvp or hunt depending in the TMs players put or how they use it.
Magcargo wont have less change to defeat fly because is not pure rock for same for ground/rock, if something is weak to x element, then x element should kill it.
Big damage and Bad HP is not something that can really work, i have had rhyperior 130 with brick and doom desire/ magcargo 130 with reflect and sanstorm and their effectivity against salamence is just really bad, I invite you to use more frecuently TEST ROOM, probably it won't give a 100% trustable answer because a real pvp all things change, but for testing damage its a very usefull tool all players have , it can even help you to report or suggest improveness of any pokemon.
If you have a true argument to fight vs mine then do it better next time.