Hello Flax,
First of all, you have brought the Arma server community a great tool here and thank you for that.
Other the issue mentioned above, I noticed that when mods are downloaded (this was the same in 1.3 beta) they do not appear in the mods list on the server setup area (local mods in arma 3 root folder such as @AliveServer do though). Is this on my end, do i need to move them manually and rename them or are they meant to display once downloaded?