Personally, I really dig having the fretboard scalloped. Maybe it's 'cause I'm such a Malmsteen-head -- if it's good enough for Yngwie, it MUST be good enough for you and me! Ha ha.
On my 777DY, having the last four frets scalloped kicks major bootie, as I tend to use those fret positions for slides or "big ending hammer-ons" on arpeggio sweeps. Having a little extra meat to dig into with the scallop makes that kind of sliding and hammering tremendously easier for me. I also find that I play in the upper registers much more frequently with the JEM than any of my other guitars.
I've heard tell in an old thread that the scallops are much more relevant on a model WITHOUT the "all access neck joint" due to the bulkier heel on the non-AANJ oldies like mine.
If you can, try before you buy either one, or before you take that dremel to your board. See if it works for you.