It seems when flipping the Relation in solid edge it changes the planar relation to a Mate relation.
So i assume the mate relation can flip but not a planar relation. Unfortunatly on the relation3D object i do not see any mate relation method possible in the sdk. I'm working with SE 5.
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.
Hope this helps,