In my mind I always pictured her as taller than MC.

I'm pretty sure she is. I thought Minato was somewhat on the short side.

Growth spurt within the year he was alive of course

Minato/MC is actually about 3 inches taller than Mitsuru according to the official heights. Minato/MC is suppose to be about 5' 7" and Mitsuru is suppose to be 5' 4".

I guess maybe it's easy to think he's shorter than her at times, like when he's sitting down or would probably slouching. (I certainly thought he would be shorter than her, myself.)

She's usually seen as taller due to her heels in the game.