apparently you cant just "patch" the os that way to make it work with coldfire for example, which speaks for apollo core compatibility.
Well, actually, one could. Except that the result would be unbearably slow. The problem with the coldfires is that they only support 32-bit math, so every word-based or byte-based arithmetic instruction would require an emulator trap. And there are plenty of them, it's really a pretty common type of instruction on the Amiga.
this is one thing. another is, that the more instruction a cpu doesnt provide without a library support, the less it is compatible for "nodos" software, that not accept being run from the operating system. of course it is usually only old games, that do not require acceleration in first place, its nice though staying compatible even with these as far as possible.
Well, the (small) Phoenix core for the Vampire (and we're only talking about this core at the moment) does not support only instructions that are barely used anyhow. First, some 68020+ instructions like some 64-bit math (only 68020 anyhow), bitfield instructions (hard to do in pure hardware, slow anyhow, and 68020 and above only), MOVEP (rarely used, if ever, but available on 68000), BCD-arithmetics (ABCD,NBCD,SBCD - 68000, but rarely ever used) and the CAS2/CMP2 instructions, which are also rarely ever used, and 68020 and above only.
Parts of the set are already unsupported on the 68060 (parts of 64 bit math,CAS2,CMP2), some parts are new, but again usually not used (BCD arithmetic, MOVEP). Only bitfields are *sometimes* used, but they are really hard to do right. Especially, they need to read up to five bytes for a single instruction, and may not read or touch any byte outside of the requested range (to avoid side effects on hardware registers). Their emulation looks surprisingly complicated, and on a "real" CPU you probably want to do that stuff on microcode, and not in "gates".
Whether the full Apollo core supports these instructions I don't know. But honestly, it is not really a loss, and providing a support library for that kind of stuff does not make the project any worse. It's mostly instructions you would microcode in a "real" hardwired CPU, but microcode is nothing that one can do elegantly in an FPGA, so it wasn't done.