I figured this out with the help of this post.
In essence T6 servers need to read the configuration out of <game_root>/main/, a directory that doesn't exist by default (but did/does for t5).
Making that directory and adding my .cfg files there allows my Docker image to run t6 servers.
I've updated the repo with this solution as well. (mkdir -p /home/pu/games/pluto_t6_dedicated_server_full/main)