I've selected a few boons and Hooks, and selected 2. The rest are below, in case people are interested.
So, I guess I'd select...
Boon: Inhuman residents. This could be ghosts from the fallen warriors, or Living Trees? Maybe a host of friendly magical spirits?
Hook: Gender Imbalance. All those men who died in the war.
Conscious Space (Major): The covenant lies in a symbolically embodied place. It is incarnate in a self-aware, friendly figure.
This could be our figurative tame noble, as well as an interesting figure to deal with. Or something yet more obscure, such as a mystical tree.
Inhuman Residents (Minor)
The majority of the residents of the covenant are inhuman.
Ghosts from the war maybe?
Natural Fortress (Major)
This covenant is all but unassailable because of peculiar geography that limits attackers to a single line of advance.
Regio (Minor or Major)
The covenant is located in a magical regio that can be entered in many ways. The covenant may take measures to limit entry into the regio, but these are never perfect.
Strong Community (Minor)
The covenfolk look out for each other to a degree that is exceptional, even compared to the strong communal focus of medieval mundane life.
This goes against Divided Loyalty, but is also very appropriate.
Ancestral Error (Minor)
One of the magi who founded the covenant made a grave error that harmed many people, or willingly performed a deeply sinful act.
To whoever send us here with so many ressources?
The castle is in bad shape
Demonic Interest (Major)
This area has come to the particular attention of a powerful demon. It does not focus its attention entirely on the covenant, but it would like to claim the souls of the magi, and their servants, for Hell.
To come back to the backstory and Ravenscroft ideas, this'd be better suited IMO
Divided Loyalty (Major)
The covenant is divided into factions, and the Prevailing Loyalty is calculated separately for each faction
Christians, Muslims, Jews... I know ravenscroft already suggested it, but it seems like a good idea, and making them all coexist in peace might be great.
Faerie Court (Minor)
There is a faerie court somewhere near the covenant.
Given the new Faeries, this could be an endless sources of them, and thus, stories, without the characters realizing their common origin. Need a giant ogre? Check. A faerie hunt? Check. A holy (appears so) man cursing sinners? Check.
Gender Imbalance (Minor)
The covenant has a deeply unbalanced gender division
Bears repeating IMO, a great flaw for this covenant.
The covenant has only one Lesser source of income, with little or no surplus.
Uncontrolled Portal (Minor)
There's a mystical portal, except that it is not under the covenant’s control. Like faerie court, endless source of stories
War Zone (Major)
The covenant lies between two powerful noble holdings that are at war. Each side requires the magi to join it.