So.... it looks like the battleMETAL version of darkplaces is from 2018 and the darkplaces version I was getting from the repo is from 2014: 20140513+svn12208-7. I thought you had modified the engine. I didn't realize it was just a newer version. This is on Linux Mint 19 though. Mint 20 and Ubuntu 20 are using newer repos, so on these distros, apt would install the newer version of darkplaces: 20180908~beta1-2. On these newer distros, you can probably run the game with "darkplaces" from the terminal or use the version that comes with the game and neither method would cause any problems.
On Linux, the itch.io app tries to run the battleMETAL_server.bat file for some reason when you click "launch" for battleMETAL, so you have to run the engine from the game folder or with the "darkplaces" terminal command and point it to the game directory with -basedir. On my laptop, the newer version of darkplaces crashed with a segmentation fault on startup. Only the 2014 version would start. So, I would probably try to use the older one like I did with beta 1, but that would cause the mini-map to flicker with beta 2. My desktop does not have the same problem. My laptop isn't much of a gaming machine anyway, so not a big deal.