Nope, you can leave the engine in the frame. In fact, it was my new build's freaking after-market Athena crap sealing washers that made me come up with this idea. I had just weeks earlier carefully positioned my bare, powdercoated frame over the engine while on it's side with the help of wife and son. Now 2-3 weeks later fully assembled I was not scratching that frame or stripping it down again. A quick study of my 1500cc Nomad and ZRX right-side bolt-off frames sparked the solution for the Honda. To me the best part was that once done, it is absolutely invisible with the tank on - that was a win/win for me since I wanted a stock appearance.
A work of advice though - do not try to install these without the blind joints up front and the threaded inserts. If these are left out, then you will not have top-end access.
Regards,
Gorodn
Here are a few more pics -