Not much to change since the basic Covenant Settlement are good enough as is. All I added is my preferred additions, workbenches, Fusion Generator and decon arch.
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Covenant is something I have mixed feelings to claim and I wish I can obtain it without having my moral compass HP take a hit or using mods.
Kept it VERY simple with my workbenches and my choice of settlement items and modded turrets.
The Clean up your corpses and robots is recommended if you want to get rid of the default turrets (and residents that you HAVE to kill due to the game's limitation) if you don't want my Covenant setup to look weird.