There are two ways that I can think of doing this in After Effects. The semi-automated way would be to create a comp with your video and the lower third on-top of it. Render it out, then replace the footage with another video file, update the lower-third, render it out. Do that over and over for each video.
The fully automated (but absolutely horrendously complex way) would be to properly automate the job using After Effects expressions, plug-ins and scripts. I've not done this way personally, but I've read numerous articles around "data driven design" where ideas similar to what you're talking about are accomplished. I unfortunately can't post links because I don't post frequently enough, but google "after effects automation" and you'll find the Adobe documentation.