The diagonal rules and the 3d rules are pretty much the opposite of what you would expect designing for computers.
The diagonal rule is to simplify human calculation and the 3d rules are so 3D doesnt come up as much- which is useful if you're playing on flat tabletop. Computers can do 3D rules just as easy as 2D rules.
Basically the 3d rules are this: Normally combat is in 2D, and calculate it that way. If your combat is explicitly 3D, such as aquatic or aerial combat, then use the DMG rules.
A square is usually considered just a square, but you can 'stack them' if you want if it's needed.