Sorry for the delay; work and life are getting in the way of my much more important hobbies.
I am working with an XBMC developer in exploring two options for accomplishing this task.
Apparently, I am the only one experimenting with the Universal Remote mode (at least, that they are aware of). The Harmony users use a multi-remote mode to accomplish this by sending the Apple Remote ID followed by one of the six original ir codes.
I see no reason why we cannot just do the same thing the Harmony guys did.
From MaestroDD:
Every AppleRemote has an ID that is sent with each button press. It's an 8bit value so range is from 0-255 (maybe some are reserved?). The remote API exposes that ID. Normally the ID is used to pair the remote with your Mac like this: Doing the "pair" thingy with the remote (something like menu + done?) increases the ID on the remote and tells your mac to listen _only_ to this new ID.
Now we're using this in a different way. Instead of only interpreting the button-code, we're actually using the button-code + remote ID (thus there are ~255*8 buttons). The Harmony (in PlexPlayer mode) sends the default button codes but with different remote IDs which are then mapped to xbmc actions (this is hardcoded in XBMCHelper).
I am working to acquire this harcoded mapping from him; so, we will know which button ids correspond to which Apple remote id + ir code.
This sounds like a viable option to me to get away from the multi-signal sequences (which has been slow going).