Actually....

Right-handed and left-handed projection matrices have nothing to do with the flipped z/y axis.

If you look at somthing created for a right-handed matrix in a left-handed matrix, it will just appear to be turned inside out. (everything will look reversed, and all the normals will be inverted). 

I thought we were talking about the exchange of the z and y axis, which I think is a very good subject. I think it would be great to have the option to flip them inside Blender, while working. I can't count the number of problems I've run into because of this, especially when exporting models with armatures and animations. Things can get crazy when you think you have everything flipped correctly, but your bones still think they are moving forward when they are actually moving up !

Great! Now all we need is a brave soul to go request this much-needed and highly-anticipated feature over at  #blendercoders :)