Yes, the entire world pipeline for ssx1 to ssx4 had to use Z up in Maya. Does not cause any problems I know of but it is a hassle trying to think in Z up and default planer mappings are reversed from what you are used to.
These differences are interesting, and show you a little about the backgrounds of the developers. Maybe.
I'd wager that systems where Y is up and Z is depth come from an illustrative background: page layouts, 2D illustrations, where the screen itself is X and Y and adding a new dimension of depth adds Z.
I'd also wager that systems where Z is up and Y is depth come from a physical modeling background, foam models, architecture, etc. X and Y are 2D as you look from the top-down, as on a map. Adding height is what adds Z.
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I'd wager that systems where Y is up and Z is depth come from an illustrative background: page layouts, 2D illustrations, where the screen itself is X and Y and adding a new dimension of depth adds Z.
I'd also wager that systems where Z is up and Y is depth come from a physical modeling background, foam models, architecture, etc. X and Y are 2D as you look from the top-down, as on a map. Adding height is what adds Z.
Autodesk's Autocad is a drafting too. They have top down orthographic view right? only need 2 axis X and Y.
-R