Another factor of limited PC-98 translations was, at least a decade ago, not much in the way of debugging emulators. The only one I know of was "Guest"'s mod of whichever emulator it was, and while his mods were certainly a push for more obscure consoles to get attention, they were a bit awkward to use.
Thankfully that's changed now: there's np2debug, a fork of the popular Neko Project II emulator, and there are even forks of that to add more debugging features, so now I have little problem hacking this game. Sure, it's no FCEUX, but I've yet to find an emulator as good as that for debugging, and it does everything I need.
Another thing is the X86-derivative architecture was quite a bit different than what console games were used to. Not even sure what consoles used an X86. Just the WonderSwan and the original Xbox that I know of. Though it's at least far from an undocumented CPU, it is still a change from the 6502, Z80 and MIPS stuff more commonly found among consoles.
In fairness, after doing Z80 and a little 68000, it's not that far removed, the principles are the same. The memory addressing is a pain in the ass, though. Of course, as you said, X86 is one of the most documented CPUs out there, so there's no shortage of help.