It uses doxygen tags in a source comment to automatically generate the pages. It's no more difficult than wiki syntax. (see http://www.stack.nl/~dimitri/doxygen/commands.html#cmdpage
for an example). Doxygen is very capable of being used for GAE. Silnarm (and I think Daniel) has added quite a lot of doxygen comments plus I add them to my own work when it's appropriate. I've been uploading doxygen documentation and linking from trac for a while now (at the release of 0.2.13a and 0.3).
There are benefits to using doxygen for the xml reference: it's an official source (ie not everyone can modify it, though patches can be sent to developers), closer to the code so it's more likely to be updated, all the benefits of having it in git, easily released with the game, no wikia ads, link to relevant code and examples.
I'd recommend the wiki by far. One source for all information (want to learn the controls? How to mod? What Military is?) that is very easy to update by anyone (GAE team busy? An experienced editor can do it for you!) is a huge plus.
From what you've said previously there's information that no one but the GAE team can provide so for reference information it's not so useful that everyone can modify it. I see the info as three parts: user info, modder tutorials and developer/reference info. The information can still be all together for the particular audience.
Now I've made a case for using doxygen I'm going to agree that it shouldn't be used
(at least not for now). This is so the xml reference for GAE and MegaGlest can be stored in the same place. Engine developers can then see how to implement a missing feature to maintain consistency (or compatability?). Currently MG is using separate pages for their XML reference. I propose to have pages for Glest 3.2.2 and then a set of pages that combine the xml (and lua?) reference for GAE and MG that have the common parts as well as the specific parts for each.
As a side note I think translations are a similar situation. There's no point duplicating efforts for slightly different wording with the keys.