Yesterday, I took a time-lapse of fog rolling over mountains in Sedona, Arizona on a manual exposure. When I imported all of the images onto LRTimelapse, there are no flicker issues. After editing all the keyframes, and loading it back onto LRTimelapse, there are sudden bursts of underexposed images, which I've tried to solve using the Deflicker setting.

Are you still using LRT4? Because this is the Forum for LRT4. Let me know.
First Thing should be to check your workflow. If the images were smooth in the camera previews and after editing you have bumps, then most likely something went wrong. It doesn't make sense to continue with Deflicker then.

Please start over: remove the sequence from Lightroom, and in LRTimelapse do Metadata/Initialize.
Then follow my instructions carefully on https://lrtimelapse.com/workflow

If you are still on LRT4 please note that LRT4 is out of support. Please consider upgrading to LRT5, you can still get a discounted upgrade on https://lrtimelapse.com/upgrade/