That's true and I didn't know of that. That said, the Amiga configuration depends on an MMU. I don't know how hard it would be to retarget it for an MMU-less system.
I frequently see it advertised as not having an MMU, but it turns out that it does...it's just that it's a new design that isn't Motorola compatible.
On Amiga, where programs typically all live in the same shared memory space, this is not a great concern for a regular user. It could be useful for developers and some specialist applications, and of course for more modern OS models.
Apollo-Core could certainly use better documentation.
I own a V500v2+ and it's an awesome board, but this kind of thing drives me nuts.
It has other silly limitations, such as the kickstart being embedded in the fpga core, which is not open source. There's no way for an user to boot to a custom kickstart; At most, it's possible to softkick one after first boot.