Silly question: setting a transparent layer for a lower third

I feel like this should be obvious, and I haven’t tried it out, but if I have a animated lower third (let’s say like a social media “like this video” type animation), which is a video rendered from aftereffects, can I set some sort of transparency so that it can be the topmost track and not be a rectangle blocking everything below it?

Yes definitely! You can export your files as MOV files with alpha transparency background and use it within a video asset.