It just dawned on me, while the actual Firefox profile manager, I guess, is not portable (I don't see how it's not, but I'll take y'all's word), the launcher can make a portable variation. You could probably get away with making the GUI for it look like Mozilla's.
Here's how it works:
If you just have the folders App, Data, and Other, it works like normal.
If you have more than one Data folder, it starts a profile manager. Data folders can be called anything as long as the first four letters are "Data". So for my wife and I, instead of maintaining two installations of Firefox Portable, we'd just put her Data folder in my FirefoxPortable folder and name it DataJen, calling mine DataNathan. The profile manager calls the profiles by their names, ignoring the first four letters.
Behind the scenes it's just a batch operation. Strip everything after the first four letters and start Firefox. Upon exit, undo the rename.
The GUI doesn't even have to be pretty. It would be cool if it had an option to create a new profile (a new DataXXXXX directory) or rename profiles, but for a first version, just bring up a box with the two names, click the one you want to load that profile.
(By profile, I don't mean the profile folder, I mean the entire DataXXXXX folder, which contains, IIRC, profile, plugins, settings.)
You could always use "FirefoxPortable.ini" and tweak it like this -
Keep two copies of the file in the main directory. Name them "nathanFirefoxPortable.ini" and "jenFirefoxPortable.ini" and just remove the name before running and add it back afterwards.