Seems like you can use the FONTCONFIG_PATH variable to point to a custom directory. You’d have to make sure the required files exist in your repo though.
Netlify has team-level environment variables, so you should not need to configure it for every project. However, if there’s some other problem that needs to be handled for each project, then that’s a different discussion.
As for apt install, we won’t be adding that functionality. You can create a build plugin that would fetch the required fonts from somewhere and store it in a specific folder, so you can re-use that plugin for each site without having to repeat your config or something - but that’s just a guess as I don’t know about your workflow to suggest anything else.