Putting my God Learner glasses on lets me see that “Spirit Cults” are a short-hand for covering a wide range of practices.
The first is as described in the RQG rules. A shaman contacts a spirit, creates a cult for that spirit, and the spirit provides access to one or two Rune spells.
A variation of this is with long established spirit cults, where a senior initiate or even a priest of an associated Rune cult is able to maintain the spirit cult.
The spirit contacted might be an elemental spirit, a dryad or nymph, an animal spirit, a spirit of some other form, an ancestor, or a hero. You name it, it is likely possible. The spirit might be a servant or accoutrement of a more powerful entity, like Lightning Boy is the lightning hurled by Orlanth. It might be the offspring of a more powerful entity, or other fraction of that entity.
Sometimes these cults are pretty much subsumed into the worship of a greater entity. Many subcults described in the Cults books fall into this category.
For game purposes, these minor cults let players gain Rune magic outside of their Rune cult, without imposing the responsibilities or other obstacles associated with initiating into another Rune cult.