If you don't mind doing your editing inside Reaper, then layer several tracks with video like you would in an image/video editor and add the "video processor" plugin to the tracks, then pick "Combine: Chroma key" from the plugin's preset dropdown.

Or export from Reaper, import into another video editor, export to a format with transparency (like ProRes).

Or try installing ffmpeg for Reaper, export to ffv1, set custom options for ffmpeg in Reaper: https://ffmpeg.org/ffmpeg-filters.html#chromakey-1

Might just work.