What tools are you referring to and why do you say they were thrown out?
Enforcer and Angel type tools, which are kinda essential to catch many classes of bugs. If you want to use 68080 features then you can't really debug them on a 68060/40 machine either.
"Thrown out" because Gunnar - as far as I understand it and have seen it re-told - does not want to support a Motorola-compatible MMU as it will add slowdowns to memory accesses. A full-blown MMU will have to sit as a filter in-between the cpu and memory, whether it results in slowdowns or not. And it seems Gunnar chose speed.
I don't see myself getting any Apollo powered product without an MMU as I know I'm by far not fault-free enough to do without the tools, and there is plenty enough sw out there that is no better.