FYI,
Most CAD systems are or were based on the drawing board, which lays the current view from the monitor flat on the drafting table.
When you look down at the paper Z is in and out of the paper. X is left to right edges of the paper. Y is back edge of the paper to the front edge of the paper. Take the drawing to the shop and lay it on the machine table and it matches.
So the problem is not the orientation of the X,Y,Z in the design tool.
Changing the default component/assemble coordinate of the design model to match the machine that may be used to manufacture the design assumes you know how the design will be manufacture when you start the design process.
It is extremely easy to add the relevant coordinate system after the design work is done. While manufacturing should always be considered during the design process, at this point in the workflow focusing on design is far more important. Many designs may be done before even deciding which one will be made or prototyped (the prototype will more then likely be made on a different machine then the finished product).