Reading this, it seems like the Z80 emulator is a Gameboy emulator and the quirks that the dev was finding with the Z80 emulation was due to it not really being a Z80 emulator?
[edit] Reading a bit more, it is an emulator-- and apparently an inefficient, poorly-written one at that.
It was never accessible by GBA games (or at least intended to be accessed, so to my knowledge no official titles did), and so the Game Boy Micro and the DS and DS Lite, which both feature GBA but not GB/GBC backwards compatibility, could drop it without causing any problems for GBA games.