Okay so a quick update. We have been running the above on our server successfully since that post was made. It's been great. However we were running it as a mod due to host limitations. This means that it was creating and using a separate folder outside of the base folder, which is fine, but my goal is to make our server as close to base as possible.
So now that Caelum is getting his new sandboxes.io service up and running, we are able to fix this issue. Technically it's still being run as a mod at the moment, but now it's somehow being tricked into thinking it's not. So now everyone will be running out of their base folder, rather than the "basejka" folder as before.
This will be better in the long run, however it may cause some headaches for those that need to get their cfg that they had been using. So...
You'll need to get your cfg from your basejka folder and move it into your actual base folder. It should be straightforward, but if you're using OpenJK, it can be confusing. Make sure you look in the OpenJK folder in /Documents/My Games/OpenJK. You'll want the openjk.cfg. This is different than those that aren't using OpenJK, because they'd be using jampconfig.cfg.
If you need help, @ me on Discord or something.