I have been attempting to set up some simple encounters but I have been having trouble with setting the allegiance through script.

(script startup basicsript 
	(ai_allegiance player human) 
	(fade_in 0 0 0 200) 
	(ai_disregard (players) true)
)

Here is what I have set up. I added the fade to debug and confirm it works. The script compiles correctly in sapien and indeed the screen does fade. My problem though is the allegiance does not seem to work neither from human / player. As a test case I tried human / covenant and that did not work either (these teams are correctly set in their respective "encounters" as far as I can tell). Additionally as another debug bit I tried the ai_disregard command but it seemed the ai would still fight the player. Could it be that changes with the MCC version in multiplayer maps has changed something about the relationships or am I missing something super simple?

If you have any insight I would love the help!

Make sure you are actually referencing the player. The campaign scripts all do this.
(script static unit player0 (unit (list_get (players) 0)))
Needs to be at the top of your script.

Then you can apply that to the player.
(ai_disregard (player0) true)

If I remember correctly, allegiance scripts do not work in multiplayer.