My main point about menu issues was that some users try creating menus from scratch and use "old" square pixel equivalents etc. Photoshop works fine with "video" sizes/pars, so why ask for trouble.
The CS6 Illustrator (rarely used for Encore) and Photoshop should be no problem. You may not be able to use the "edit in Photoshop" from Encore if it is not the same level. If not, you just have to edit outside of Encore and reimport. Encore keeps its own version of your menu inside its folder structure. Don't mess with that one independent of Encore.
I also expressed my dismay that DVD menu button states are still one-color + alpha channel. Hard to believe this is much of a saving compared to the video load a DVD carries. How much bandwith does a rollover bitmap really take?
DVD is still just DVD and the specs have not changed. Bluray does provide some of the options you want.