@Cernel I don't see the current patchwork is a problem (it rewards the minor allies for participating). But you could easily create an event that triggers in the current version of the engine, changing ownership to reflect the assigned sphere of influence.
Here is the reference from POS2
changeOwnership values: This will change the ownership of the territory, either directly or by conquering the territory (there is a difference). Format is "territoryName:oldOwner:newOwner:booleanCaptured?". territoryName can be "all", and oldOwner can be "any". Can have multiple instances. examples: <option name="changeOwnership" value="South France:Germans:VichyFrench:false"/> or <option name="changeOwnership" value="all:Mongolians:Russians:true"/> or <option name="changeOwnership" value="Danzig:any:Germans:false"/>