Remote Buddy itself does not stream any audio to an Airport Express. 
Its AirPort Express support is limited to selecting/deselecting 
AirPort Express speakers in iTunes' interface.

The IR receiver in the Universal Dock is not accessible by a computer, 
since it's not available via USB. It thus can't be used by or with 
Remote Buddy. Please see the Remote Buddy website for the full list of 
supported receivers and remotes.

The Apple Remote can't be reprogrammed (by any software). It's just a 
simple IR remote control.

BTW: Remote Buddy is not about reprogramming the hardware of remotes. 
It doesn't, can't and really also shouldn't do that. Remote Buddy is a 
MacOS X application executing defined actions on the Mac computer when 
it receives a button press/repeat/release event from a supported 
remote control.

Best regards, 
Felix Schwarz