Hi there CJ.
I've just tried out your idea using my POD2 as the external unit and it works perfectly - and sorry Pete, no inherent latency, you must be disappointed.
First I imported a clean guitar loop into GT3.
I ran a lead from the headphone out on My TonePort to the input on the POD; I then connected the POD's output to the input on the TonePort.
I armed another track and started GT recording - this allowed me to use the POD to process the clean signal in real time while the processed signal was recorded back into GT. I fiddled around with a few different amps and effects with the POD just to emphasize the differences between the two signals.
HERE'S THE RESULT - the left channel is the original clean loop and the right channel is the processed signal.
CJ - this is a really great idea you had - I must experiment some more!
Steve