After thought
Port 993 is an "Officially Registered" port with IANA for use with SSL over IMAP. It's not like they'll be able to reclaim it for other uses if Apple stops using it for it's intended purpose. It's already done. I can understand not wanting to set a precident for unnecessary use of extra ports, but this one is so widely used. It's almost like one engineer read the referenced article and decided, on his/her own, to eliminate this port in Profile Manager, without consulting anyone else working on other projects that have used 993 for years. I'm also having a hard time with them initially not being aware of the issue and then being able to cite the exact reason why it was done the way it was (though likely they weren't the engineers who worked on the exact project).
I am absolutely not trying to kill the messenger here (obviously not your fault -- at all), I just hope they reconsider this. I think a lot of people are holding off on fully implementing profile manager becuase it's still so buggy and needs fixes. But when it starts getting more widely used, they're going to have many, many more complaints about this one.
I can just see the department-wide email now from the engineer to other Apple developers/engineers, "Hey guys, I've been getting a few calls about a change we made in Profile Manager recently. A couple months ago, we eliminated the ability to configure profiles with port 993 (SSL / IMAP). Are we all cool with that? Forgot to tell y'all earlier. They can sitll use 143 though. So, it's cool, right?"
And one typical reply: "You bleeping bleep-hole, you did WHAT???? Are you serious, or did Jim in accounting put you up to this, becuase I wouldn't put it past Jim to pull a prank like this. You tell that S.O.B. that he had me going for a few minutes. You do know he was the one who left that second iPhone, the i5 prototype, in that second bar, right, on purpose? Don't tell anyone though."