Those values are correct. I'm not sure what you are expecting. There is always going to be multiple euler sets that will yield the same angle difference. The vector/rotation alternative will also yield the same value for multiple sets. For example, the vector/rotation difference between the following sets will be the same:
Code:
euler1 = [0,0,0]
euler2 = [90,0,0]
#Vector difference will be 90
#Rotation difference will be 0
euler1 = [90,0,0]
euler2 = [180,0,0]
#Vector difference will be 90
#Rotation difference will be 0
From your first post it seems you are interested in the relative error between the two orientations. I don't see how having non-unique solutions affects this. Maybe I'm misunderstanding your original request.