Well MC is short for Maria Clara. In the game, MC is from the Philippines, and Maria Clara is a popular symbol, often seen as an ideal depiction of Filipino women. Its just a nice reference to that
I’m pretty sure MC stands for main character? It’s common to see in many visual novels for the protagonist if they’re nameless to be referred as mc,i don’t know if their intention was to use like, a double meaning with Main Character and what you said but i don’t think most people have read MC as Maria Clara tbh If they were to name the protagonist María clara i think they would have had no problem saying it outright since they had already established a nationality and a physical appearance. I think some things are purposefully left vague for people to relate a bit with the protagonist Imo