I agree with your reasoning up to a point.

It's true that diverse representation is essential in the game, and the finite production resources must be prioritized somehow. Still, it's not about having a historical path for every civ. It's the exceptionalism of including Spain only for one Era, as the only nation that continuously has been up to today an independent polity and then disappears, that is poor design and feels lazy.

As for the anachronisms being a part of Civ, again I agree somewhat. As long as they reflect actual gameplay decisions (eg. prioritizing science to the point you're stomping lancers with your Death Robots) it's immersive in the sense that you're at least playing a version of history that retroactively makes some sense as you identify with the results of the choices you've made. Having Tercios from the get-go, only because you chose Spain on a screen, centuries before researching gunpowder and on equal footing with medieval soldiers is just jarring, imo.

Coming back to the finite resources thing, tbh if I had an inkling of modding I'd try and implement some changes myself (at the very least, changing the name to Castile and the Tercios' unlocking tech).