Popup responded via email:
Most of the controls and setting on the 990 are present on the 2080 but either expanded. There are lots of new controls too. I think any shared Sysex would kind of be a fluke but need to investigate to be sure.
In short, I would say that you can use the 990 layout only as a skeletal structure to for the basis of a design for the 2080.
Also, in a separate, earlier response:
I remember talking somewhere about the 2080 before. I had a 1080 for years and ended up swapping it out for a JV1010 because it had the same engine but was only half a rack in size. I actually started a JV1010 layout straight after the 990 but remember quickly realising the increased scale and complexity. There would have been a way to do it if certain features were available in MD but that would have also limited the creative freedom that made the JD990 Layout work so well. Making a complete 2080 Layout is still be a challenge I would relish, the resulting layout huge!
You can imagine my surprise and interest when the task of attempting a layout for the Fantom XR layout was bravely taken on by Elkbeat. The Fantom is a further evolution of the JD line of Synths and even more complex. I just could not see any neat way of handling the depth of the whole engine.
As it turns out, he did not. He went with the sensible route, designing a well balanced and great looking layout without digging too deep into things. I have a great deal of respect for Elkbeat and the thought that went into deciding where to draw the line.
Popup is quite busy right now, but at some point in the future he might attempt this.