I use them as well. I think the zirconia bur will just work well on the softer wax after a lot of use in zirconia. I can tell you that if you use them backwards you're in for a world of disappointment in your zirconia milling. I got the switching order mixed up and a worn out Zr bur that is used on wax, and then switched back to Zr just does no one any favors.
We use similar in our Wieland Mills. The Basic burs are the same bur, you just make the distinction in the CNC Software so that the mill will not pick up an instrument that has been milling WAX/PMMA and start milling Zirconia. As doug says, it "does no one any favors."
Now our single edge cutters are only for Wax/PMMA, and our Diamond or Titanium Nitride coated cutters are only for Zirconia.