jaycat, you are understanding how the pedal works. It requires the chord accompaniment in real time to determine what harmonies to apply to the vocals. It will actually add the effect to anything picked up by the mic, but as you surmised the mic in the video isn't picking up enough uke to matter.
The reason you only see it used live is that most people will sing and record a separate harmony track when they are in the studio. You'll get a much more pleasing result than the synthesized effect from the pedal. That's what I'd recommend--record the guitar part, record the separate vocal track, then record a separate harmony vocal track.
If for some reason you can't or don't want to sing the harmonies separately, then you would either need to a) play the guitar along with your vocal track that is running through the TC Harmony pedal (and try to minimize the amount of guitar picked up by the mic), or b) figure out a way to run the previously-recorded guitar track out from your interface and into the pedal while you record the vocals.
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