@Friznit Well the first issue is of course it's Steam Workshop only, which I understand may be problematic if you run a Linux server.

Don't know how much of a common knowledge it is but use programs such as psftp to transfer files between the server and any other computer. One can find psftp along with a program called "Putty" here: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

I personally use psftp to transfer Arma 3 modifications (such as Iron Front lite) that are only to be found from Steam Workshop. One just needs to find the hidden !Workshop-folder where all the Workshop files go. Somewhere around here --> L:\Steam\SteamApps\common\Arma 3\!Workshop