Tested with Surviving Mars + Surviving Mars Mystery Resupply Pack DLC. The prefix dir was initialized with only the Surviving Mars package installed. The DLC package was then added, and on the next start the DLC content was available in game and the symlinks correctly created on disk for the new content. Multiple starts did not cause any issues from the auto rescan on startup (i.e. no duplicated files/symlinks/etc).
Original pull request on GitHub: https://github.com/vv221/play.it/pull/24