Because the designers wanted it to work that way, and that's the best answer you'll get. D&D Hit Dice have
never been exclusively about toughness, but have always included all the other nonsense about fighting skills (attack matrix/THAC0) and defensive prowess (saves). Connecting skills to it as well was logical, because it's already at the core of the system for monsters.
The first priority of monsters out of the MM is that they should work straight out of the MM.
In 3e, a second priority was that they should integrate with class levels. In AD&D, you'd often see phrasings like "There are four minotaurs here, lead by their shaman who has the spellcasting abilities of a 4th level cleric of Baphomet." In 3e, that'd instead be a minotaur cleric 4, and the system is designed to tell you exactly what that means.
But when 3e was first published, making a minotaur work
as a PC was by no means a priority. Making it work
like a PC was.
1. It results in the preposterous implication the the CR of mirror fight against a creature with the same stats would not be an ECL appropriate encounter
CR and ECL are nowhere near the same thing. In an ideal world, CR measures how difficult a monster is to fight for a few rounds, while ECL measures how strong this creature would be as a PC under ideal circumstances. Just to take a really easy example, say you give a monster Fast Healing 1. That's pretty much a non-ability for a monster, because at best they'll get something like 5 hp more out of it over the course of a fight before being brought down. But it's an
amazing ability for a PC, because it means you more or less enter every fight at full hp without taxing the healing abilities of your party (now, you pretty much did that anyway due to the unintended consequences of
wand of cure light wounds, but I don't think that was ever intended by the devs).
IME, the PF2/4e approach is better, but it does basically boil down to making variants into entirely different monsters mechanically.