For example, the built-in IR receiver can be set to only wake the Mac 
from sleep on button presses of a particular remote. That feature can 
actually be very handy, but it's only possible if the receiver also 
interprets the signals it receives.

On the other hand, a receiver that just passes on raw data would wake 
on every IR signal, including those of your stereo, TV, etc. - which 
can become annoying pretty fast.

So, I guess that the built-in IR receiver can only be used with Apple 
Remotes is the price that has to be paid for that kind of convenience 
features ;-)

Best regards, 
Felix