This makes a huge difference. I really wish the Axe-FX had a good way to copy or use Speaker page presets, since on the 11R that's essentially what I have access to.
Based on the above 11R experience I went ahead in the Axe-FX and manually set the JCM800's Speaker page to the values found in the AC-30 model. Time consuming, but it made the JCM800 way more enjoyable for me. This to me is a big problem with the Axe-FX: you can easily change out your speaker IR, but without tedious tweaking the power amp will still interact with it as if it were a different speaker.