In the documentation i found the following information that the property NormalsAligned defines the orientation of the faces:
This relationship makes the planar face of a feature on one part parallel with the planar face of a feature on another part. The placement of this relationship is limited to the interactive environment. Once placed, however, you can use automation to modify the offset of the planar alignment. Also, from this object, you can access information about the type of relationship and the associated parts. The interactive user places PlanarRelation3d objects using the Mate and Align commands. A mate and planar align are the same except for the orientation of the faces, which is defined by the NormalsAligned property.
As you noticed, yes, changing the NormalsAligned property on the planar relation is the method for Flipping the relationship. There is a sample program delivered in the Custom folder called 'SEAssemblyRelationshipBrowser' written in VB.Net that is a very useful reference for using the assembly relationship API in case you haven't seen it.