I wrote an entire paper in college analyzing the geology of the Misty Mountains and to a lesser extent the White Mountains (the Misty Mountains are easier because we get a cross-section via Moria). One thing I discovered that still knocks me for a loop when I think about it is:
Moria is the only place in Middle-Earth where mithril is found, right? That's kind of a big deal. So, why? What makes that location so special? Is it just random?
I found a paper that had just been published *that year*, 2011 or 2012 as I was writing it, that studied the locations of precious-metals mines in the Pyrenees, the similarly long skinny mountain chain that divides Spain and France. This paper discovered that where there was a bend in the mountain chain, from one of the continental plates having an awkward corner in it that got subducted under the other plate, that had dug deeper into the mantle and caused precious-metal-bearing ores to flow up to the surface in ways they didn't do anywhere else in the Pyrenees.
There's a conversation in The Fellowship of the Ring where one of the hobbits -- I don't have my copy handy or I'd get the direct quote -- asks why they can see the Misty Mountains ahead of them at one point if they're still heading south from Rivendell, and it's explained that south of Caradhras (which you may recall is the surface mountain under which Moria runs) the mountain chain bends and runs southwest instead of due south for a while.
Tolkien had absolutely no way to know *why* this particular feature of a mountain range was associated with intrusions of rare and unique metal ores, but he had gone backpacking in mountains enough to know How Things Should Look.
(And as prev excellently points out, when Jirt made screwed-up geology it was very much on purpose. Mordor shouldn't be square! Mount Doom shouldn't be doing any of the things it does! A composite volcano shouldn't even have especially hot lava! Even the Gulf of Udun, the circular feature at the upper left corner of the square, shouldn't be like that -- perfectly round features should be impact craters or calderas, not The Mountains Just Do This In A Suspiciously Convenient Way. These are all the way they are because Sauron forced them to be, in defiance of the laws of nature. Remember, he's akin to Balrogs and was a Maia of Aulë -- he's a volcano spirit in many ways.)