I'm not sure, but isn't there problems when replacing files from a debian/ubuntu package ?
I don't know either. Actually I only told half of the truth, since /usr/share/games/openarena is the place for the
openarena-data package, so the binaries there will be ignored, only the pak6-patch085.pk3 does count. The
binary is in /usr/games/openarena, don't know if you overwrite that one your config is still found or not. But I think if you place an executable bash script called openarena in your ~/bin, then you can actually use the new binaries in the /usr/share/games/openarena folder:
#!/bin/bash
cd /usr/share/games/openarena
./openarena.x86_64 $@
It's a plain text file, save it into your ~/bin folder, and make it executable. Replace ./openarena.x86_64 with openarena.i386 if you use a 32bit Ubuntu. After that if you issue the openarena command, the new binaries will be launched. I use this method on Debian for running the game from a shared NTFS partition. Symlinking could also work, but I didn't have luck with that.