The Code vs controlling land as a covenant

The Promises mini-adventure available for free download is pretty explicit that having a charter from an abbey granting land rights in exchange for possible services later is a serious breach of the Code. I assume that it's the latter part (promising services, and in this scenario's case, having already provided a magical stone) that is the real issue rather than having been given land.

Certainly, all the language in the Covenants book suggests that it's very standard for a covenant to be the equivalent of a small landowner with control of mundane land and the people on that land. That's the way the covenant earns its mundane income. But how does this arise in the first place? Surely some higher mundane authority must have been OK with this situation coming to pass, and that sounds like some sort of charter (formal or informal) being granted.

Or is it that covenants are founded in the middle of nowhere where no mundane authority has any claim (if such places even exist), and that the covenant then attracts peasants and the like to do all the hard labour, and to link the covenant into the wider mundane economy.

Is there an angle here I'm not seeing?

There are several options.
In the middle of shifting political landscapes such as often occur in medieval/mythic Europe, there may well be land which is contested but not necessarily valuable where magi could slip in and establish a covenant and rely on competing interests to allow them their own degree of sovereignty.
They may be given land which has inherent duties not necessarily promised to an outside entity. For example, this lord has amongst his estates a piece of land with a large and dangerous magical beastie inhabiting it. Contribute the land to a covenant and the problem is solved.
There may be places where they can gain the rights to the land with no more obligation than would be expected of any unpledged occupier of the land- having to pay rents for example.
They may make the land.
They may occupy a bit of wilderness which may well be under someone's nominal rule but where nobody goes to check on things.
Land may be granted as a buffer between enemies.
Land may be granted to create an informal obligation- donate the land for a period of 5 years after which time the grant must be renewed...

I do have to wonder though about this explicit prohibition- my impression has been that the rule against becoming a court wizard or pledging service to a noble did not apply to the Church...

They do exist, in most of Europe (one notable exception being England, after the grubby upstart William the Bastard conquers it in 1066); they are typically called allods.

Exchanging ongoing magical service for land is forbidden. Performing a service for land is less clear. Expanding on something Silveroak referred to --

Example: A duke has nominal claim to a valley, wherein an ogre slaughters all who pass by. The ogre prevents farming; no villages can survive there, and the pass is cut off. Slay the ogre, oh magi, and the land is yours, subject to no tax for twenty years, and you may charge a reasonable toll for use of the road.

Example II: A mercenary Flambeau decides to settle down. He offers a lord forty days of military service of a sergeant and a dozen footmen, annually, for that section of wasteland the villagers say is haunted. Offered a chance for something from otherwise useless land, the lord accepts, and the grogs (or just a band of mercenaries) provide the service. The lord doesn't care very much, at first, that the strange but dangerous mercenary has little trouble on those famously haunted moors. In forty years, his grandson may become interested.

I agree with Fafnir; the other exception is Sicily, which has also been invaded by Normans.

Thanks for the examples! Allods aside its great to know that covenants can indeed slot themselves into a medieval hierarchy without immediately violating the Code...

If in doubt, fake it - there's a reason that "Faux Feudalism" (having a tame nobleman who holds the lands in your name, while all the resources go to the covenant) is listed as a free choice in Covenants. It's there as a handy option if you wish to explain having the trappings of nobility (castles, large landholdings, expensively armed grogs) while not being bound by oaths into the local feudal system.