huh....first I've ever heard of a Architectural Engineering PE. Tried reading about it online, but I can't figure out what they do exactly.
I can't answer for everybody's job description or motivations, but I can share my personal perspective/thoughts: AE PE's are generally individuals who are (A) working somewhere in the building construction industry and (B) who are to some extent "cross-discipline" in practice.
The AE PE exam is unique in that each question is specific/applicable to engineering within the commercial building/construction industry.
Our engineering design and skillsets are not limited to any single discipline. I can run loads, size HVAC/plumbing equipment, pipe/duct everything up, select and lay out lighting fixtures power/telecomm outlets, draw up risers and control schematics for all trades, and assemble the specs. I'm versed in NEC, common building codes, energy and ventilation standards, and so forth. That said, I do not touch structural with a 39.5ft pole, except on rare occasions where a quick reference to my steel manual can provide general guidance.
In practice, I will cover all MEP trades for smaller projects, but will commonly split the work with one or more other designers for larger/complex projects. For example, I'll take on the role of "the electrical" a given project and focus on that piece of the pie, allowing me to devote more time and attention to afford a more complex design. The trades I pick up for any given project varies with the individual(s) I'm working with and what holes need to be filled.
An AE PE is likely NOT designing utility power plants or chiller internals. We're not sealing drawings for a suspension bridge. There are projects in the broader building/construction industry that do require a specialist, and it's on us (as with every PE) to follow the NSPE code of ethics and only seal/sign items falling under our area of competence.
Our cross-discipline background definitely helps us in certain aspects including energy modeling, project management, CA, and design coordination meetings.
I recall from my job-hunt years ago that some employers actually discourage cross-discipline experience/practice in all or part of their workforce ("you're either mechanical OR electrical"). I suppose in such an environment/culture you'd have an uphill battle to pursue or even consider a multi-discipline license. If you reside or do most of your work in one of the states who doesn't yet recognize the AE PE, I could see that turning you away as well.
I don't have the life-experience yet to know how everything might turn out, but I anticipate my past and on-going cross-discipline CA/project management experience one day will not hurt my chances at climbing to an upper management role.
Again, this is just one young PE's view of the situation. I'm certain individual experiences and circumstances drive others to pursue the AE PE (or not), but for me it seems the best fit as it's the exam whose contents most closely match my actual areas of competence and practice, in addition to my future career goals. I live & work in a state which recognizes the AE PE, which I suppose helps from a marketing perspective, but I continue to design for projects all over the country in states who do and don't recognize the AE PE (in which case an ME and/or EE in our office can review and seal my work).
As an aside: I've noted through wikipedia that the term "Architectural engineering" means very different things as you cross borders into other countries - I gather building engineering of all disciplines and general architecture practice can be one and the same thing in Japan, for example.