I'm going to dissent on the memory protection thing for three reasons: first, technical: CAOS probably wouldn't have been as efficient, expandable, and pleasant as AmigaOS assuming it made a serious attempt to implement memory protection. AmigaOS was those things because it had a message passing architecture that relied upon each process being able to see each other process's data. This worked throughout the entire system, device drivers passing disk blocks to file systems ("handlers"), in turn passing that data to running programs.
The first Amiga designs also barely supported memory protection. The A1000 had hardware in it (which I don't believe was part of the core Amiga chipset) to write protect a block of memory, but that was it.
The second problem is that CAOS was ditched for AmigaOS with Tripos for a very good reason that would have also hit Atari - it was too big a project, and they had a deadline to meet.
The third is we kinda know what choice Tramiel would have made to deal with the deadline issue, because we know what he did for his own Amiga rival: he would have said "We don't need some Unix like system, people are using PCs, they're happy with single tasking and 8.3 filenames. Let's see what Microsoft's rival Digital Research can sell us"
And the Amiga would have run TOS - essentially a first draft of DR's DOS Plus operating system, with GEM.
I do agree that Atari's management would have worked better for it in the longer term, but I think Atari's Amiga A1000 would have been a whole lot worse than Commodore's.