both "philosophies" have advantages and disadvantages. The mixture of 68k and PPC sometimes creates problems that can be avoided by not mixing both. And as far as I know this direct mixing only works because of using PPC and so making it even more difficult to change to another platform. So both ideas are not better or worse, they are different with advantages and disadvantages.
The main advantage (what I have read) of direct integration like on MOS/AOS is that 68k environment directly make use of improvements of the new libs and it should run a little faster. But for me (when I developed the distribution) it would have been a nightmare because the main libs change all the time, there are different versions of different distributions used (propably not everyone update it immediately so i would need to test it everywhere) and there are different processors (68k, ARM, X86). Now i have a defined environment.