I have a timelapse of the aurora, shot from a tripod in a static position. Several of the frames captured headlights of passing cars. Since the headlights only affected the foreground, I can fix those images in PhotoShop by replacing the sky. However I don't see how to export the fixed images in a format that LRTimelapse can use while evaluating auto transition, visual previews, etc.

I could use the original images with the headlights, then fix them in PS and replace the final .jpg or .tif images before rendering a video, but how can I ignore those original images so they don't affect auto transition, etc. Sorry if this sounds confusing, I'm new to all this!

Just do it the other way round. First edit everything in Lr+LRTimelapse.
Then export the Intermediate Sequence in .Tiff Format.

Take the „bad“ images from the Intermediate Sequence and edit them im PS.
Save them as .tiff and render the final edits with the LRT Renderer.

Thank you, that makes sense. My question about that process is, how do I prevent the "bad" exposures which are much brighter due to headlights, from affecting the visual luminance, deflicker ramping, etc.?

You can edit the few exported jpg or tiff files in Photoshop prior to rendering the video file in LRTimelapse. I usually copy the exported file folder before making edits just in case. Save the edited files with the same file name so LRTimelapse will recognize them.