umen export templates are in fact headless Godot engine (the core without the editor) and embed all features including 3D, physics, etc
Compiling your own means removing what you don't need, create your own template which will be packed in exported package.
Engine is provided with game because... how to deal with GDScript code and nodes structure you've made ? It's interpreted code than a compile code. Quite like java or so BUT with a local VM dedicated to each project instead of being shared.
It's nothing to do with being logical or not, it's a design choice.