>>55406051A. To balance out Pokemon while meeting BST benchmarks. Mewtwo having only 570 BST doesn’t sound as impressive and Megas always are +100 in BST (besides Alakazam in Gen 6 that was an oversight)
B. To still allow for flexibility. Pokemon often invest into their higher offense, but plenty of Pokemon could do either or both for different reasons. Mewtwo could used Physical Attacks to beat Blissey and synergize with Curse for Gen 2. Kyurem-B could run special sets back when its coverage was shit on the physical side. You also have mixed attackers like Infernape as well.
C.Pokemon is an RPG meant for children too dumb to know how stats work. If a kid wants to run Flare Blitz + Fire Blast on their starter, they can and both will do good damage.