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PC-98 was a series of x86-based Japanese computers that offers Kana-Kanji support, which shared some hardware similarities and operation systems with IBM PC, and software was relatively easy to port between the two architectures. But the two architectures were never compatible.
What technical aspects in hardware and software make NEC PC-98 architecture incompatible with IBM PC architecture? (Not to be confused with the reason why NEC chose to differ.)
As both share the same CPU architecture which has a dedicated set of support chips, both the IBM PC and NEC PC-98 platforms are built from same or similar building blocks, but the design how they actually are connected together and to which addresses is different.
At least it has the following differences
BIOS implementation is different
C-bus instead of ISA bus
support chips are at different IO addresses, even if most basic chips are of the same type
memory map after the 640kB base memory is different
Interrupt and DMA channel usage
Video interface done with NEC UPD7220 chips
This means that any program which uses the hardware directly instead of using DOS calls will not work on both architectures without porting over the code which accesses the platform specific hardware.