The same way you add new items to the server from ARK's updates.
Just use the engram names to enable the ones you want, and skip over the ones you don't want to use, which will then not appear in the game.


IE:
OverrideNamedEngramEntries=(EngramClassName="EngramEntry_New_Stone_Stairs_C",EngramHidden=false,EngramPointsCost=5,EngramLevelRequirement=20)
OverrideNamedEngramEntries=(EngramClassName="EngramEntry_Rounded_Stone_Stairs_C",EngramHidden=false,EngramPointsCost=5,EngramLevelRequirement=20)
OverrideNamedEngramEntries=(EngramClassName="EngramEntry_Rounded_StoneWallWithWindow_C",EngramHidden=false,EngramPointsCost=5,EngramLevelRequirement=20)
OverrideNamedEngramEntries=(EngramClassName="EngramEntry_Rounded_StoneWallWithDoor_C",EngramHidden=false,EngramPointsCost=5,EngramLevelRequirement=20)
OverrideNamedEngramEntries=(EngramClassName="EngramEntry_StoneRoundedWall_C",EngramHidden=false,EngramPointsCost=5,EngramLevelRequirement=20)
OverrideNamedEngramEntries=(EngramClassName="EngramEntry_RoundedStoneRoof_C",EngramHidden=false,EngramPointsCost=5,EngramLevelRequirement=20)


Just open up your ARK folder on your local machine
~\SteamApps\Common\ARK\ShooterGame

Then use the lil Windows Explorer search bar and enter:
EngramEntry_

This will bring up every Engram name currently in ARK, including mod engram names.
Then just do the normal game.ini thing EngramEntry_NAME_C and plug it in to your game.ini with the overridenamedengramentries= crap.

--

I also use a custom game.ini for engram listings. Though I do not run a primitive server, I restrict some of the top-tier stuff like auto-turrets and rocket launchers.
So I have to do this as well each time I want to add a mod, or each time ARK updates and adds a new item in that will be approved on my server.

Wow, thank you so much for this post! I was literally posting a request for Engram Overrides in every mod i use discussion forum.