Except that nobody is following the Z up coordinate system rule outside of Max, not even us. 
Krakatoa Maya writes PRT files as Y up. Naiad writes out files as Y up. Have not looked at what RealFlow does, but I suspect their PRT files aren’t Z-up either…
You are right that we need a solution, and it should be a hint in the metadata, so the loader knows what to do with the incoming positions.
When loading BIN files, the PRT Loaders in Max and Maya flip the left-handed coordinate system to right-handed, Z or Y up, because we know what the BIN file specification requires.