Well I managed to find a really old patch against 2.03 that adds in support for the PC-98xx.
It took a while to get a working environment - the patch was a partial binary diff against libc.a, which would work on the version of DJGPP that I found, so I had to bootstrap the whole thing from within Dosbox with a correct version of GCC (2.95.2, if you're interested!).
Finally got it all running and compiled binaries can run on both regular PC MS-DOS and PC-98 MS-DOS as long as you have a DPMI server for the latter (cwsdpmi wont work, quite obviously, but there's one by Microsoft, on the PC-98 DOS 5.00 floppies!!!).
Anyway, I can see there are a couple of efforts to get full support in current versions of DJGPP, but for now there's a pre-built Dec environment and how-to on my wiki:
https://www.target-earth.net/wiki/doku.php?id=blog:pc98_devtools
Next step is to work out how to talk to the custom NEC graphics hardware from within GCC+DJGPP...