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And don't forget that Middle-Earth was transfomrd from a flat world to a spherical one after the invasion of Valinor by Ar Pharazôn, which may have resulted in some deformation of the surface.

Also weren't there big stone giants living in Misty Mountains (even in the Hobbit movie there was a scene with them I think)? So that could explain a lot of inconsistent geology as stone giants could do a lot of "terraforming" during their battles. Over thousands of years they could have reshaped the original landscape.

I think you mean the Blue Mountains not Misty Mountains right? According to the map in the Silmarillion they were the Eastern border of Beleriand.