AOS 4 works in the SAME way. It has partial memory protection (as does MorphOS) to protect UNALLOCATED memory and some SYSTEM memory areas ONLY.
Switching to an isolated address space for each app would absolutely KILL performance since not only would we need a new message-passing system like QNX uses, but we wouldn't be able to use shared libraries. IIRC UN*X, and its clones load a separate copy of the .SO file into each address space so it wastes a TON of memory. Windows and MacOSX are no better when it comes to memory management.
In short: Amiga is fast and performs well BECAUSE it doesn't use full memory protection. That's the hand off. Do you want security or do you want speed?