Alpha Centauri had some terrain modification in a 4x game (real big bombs, construction units that could raise and lower terrain, and “melt the ice caps”), as well as a super simple weather model that could kind of interact with it (iirc the prevailing wind always came from one direction, but you could raise or lower a ridge to make it wet or dry in an area).

Influencing continental drift for strategic purposes would be hard to justify in a realistic/up-to-near-future game, but sci-fi is always there. Or maybe someone needs to try something new, like a 4x game that takes place on an evolutionary scale. Synapsids & Sauropsids. “I‘ve got you down to your last Lystrosaur, bwahaha”

There is: developer time and focus. Not everything needs to be gamified and have "player retention", etc.