I've encountered an problem with uploading videos. The colors look fine in the source video produced by lrtimelapse, but then when I upload (doesn't matter to where), the colors have shifted and appear washed out. I figured out a work-around by exporting the files from quicktime, which converts them from .mp4 to .mov. Has anyone else encountered this issue?

Most upload services will convert the videos once more. LRTimelapse video output is normally meant to be used as masters for further editing, not for direct upload. The output have much higher quality then the services will directly play back.
The color shifts could happen because of the conversion not taking into account, that LRTimelapse by default produces wide color gamut files. Please try setting the Color Gamut to Standard in the LRTimelapse render dialog, if you want to directly upload those files.