The why is because Amiga isn't his target audience.
You may not have to recompile FPU software, but that doesn't mean it produces the same results. I'd like to see that said first.
Does Majsta and the Apollo team have different goals? From what I've seen, and it's probably a very incomplete view since I haven't really delved into it, it seems like Majsta wants to make accelerators for classic Amigas while the Apollo team seems to view Amiga compatibility as just a starting point with the goal of a standalone, Amiga-ish machine. Sort of an Amiga plus (or perhaps minus depending on your point of view).
I could definitely be completely wrong because, like I said, I haven't really dug into it much. If it is true, maybe it's unfair / wrong to discuss them as one and the same?