Mono version is about twice as big. Also UWP is not yet supported with Mono. Also I think only with 3.4 will Mono be out of beta and considered stable and feature complete.
Godot is all about avoiding bloat, so if you're not using C#, it's nice to be able to not have it lingering around at all.
Maybe Mono and GDScript can be moved to plugins in 4.0, so everyone has one base version and just adds the scripting language they want.