I'm aware of the preview support for Time Machine over AirPort Extreme. It was one of the reasons the user-community was so ripe upon final release when, for no apparent explanation, support was pulled and evaporated from all documentation.
Regarding the pure speculation of AFP-requirements mentioned previously. Um. they're not speculation. Did you even read the documented requirements for a Time Machine Protocol-enabled AFP server that Apple released? (and that documented list is NOT complete, btw).? Lion requires an AFP implementation not provided by the AFP services on a APE. There is no reason they are not provided apart from the simple fact that Apple chose not to put them there. This is inarguable. Speculation dawns from the reasons for that decision, and I grant you that. That speculation is not, however, founded on thin air. I've done my homework on this. It is because Apple has chosen to do things like the yanking TM support in an APE at the last minute before release that I even bothered. If, however you have an alternative hypothesis that is anything besides devil's-advocate throw-back I'm always interested in hearing a differing opinion.
Regarding Apple's "support" for NAS ? If by "support" you mean they don't outright cripple it intentionally? I concur on that. However, doing that often leads to nasty and prolonged time in court rooms (read Adobe PM vs. Microsoft). Apple can, however, freely cripple their own hardware and software solutions which they have every right to do so. Obviously they're free to do that, though it becomes, IMHO, unethical the moment they do so after pimping their intent to do the exact opposite in their prerelease material. That has shades of the tales of old when vapor was marketed to squelch potential competitors from even starting to develop alternatives.
Apple does release their updated specifications for new features in AFP (currently released is 3.3) which I completely support. It is wonderful thing when manufacturers release all the goodies to assist you in intermingled product development to make your stuff work with their stuff. However, that they don't document all the features in that protocol and furthermore utilize those undocumented op-codes within their own solutions is something I most certainly do NOT agree with. Those were the kinds of things that chapped the hides of Windows engineers 20 years ago and fostered the ludicrous claims from MS that they never used undocumented functionality from their OS for non-OS-related advantages (read: Office). It was easy to prove otherwise back then with a few minutes on the business end of SoftICE. It is still so today with AFP and simple packet decoder tailored for DSI wrappers around AFP commands. Literally any software engineer can demonstrate that AFP out of a Lion client uses at least one undocumented op-code (no undocumented DSI that I've seen, however, so props for at least that).
Finally, regarding the case of the two devices. The internals of the case are the same. the dimensions are widened on the physical case of the TC to allow slipping a hard disk inside. other than that they are functionally identical (save for the masked-off pin-out for the SATA controller, which is not present in the APE.
I love my Mac. I always will. It is beyond-superior to anything in its class for non-Mac solutions. When given the choice for buying a new laptop you couldn't get me to the Apple Store web site fast enough. They just work, and I love that. Being an old-school Unix guy (BSD at that) made it even more attractive. Out of all those choices out there I chose Apple because I wanted it, not because there was no other choice. How I wish supporting that decision was as freely distributed in choices.
All that being said, perhaps Apple will shock us all and update the APE firmware to allow, and more importantly support, this wonderful feature again. Or perhaps their next line of APEs will have it available. Perhaps. But all that would do is cannibalize their own market share for Time Capsules for no real win, so I'm not going to hold my breath on that one. Never say never.
Good luck to you all out there, and have a pleasant day.