Hmmm. So perhaps I should try using ICL and see what happens.
As there doesn't appear to be a clear answer as to which is "correct", it occurred to me to ask 'which is better'? In that context, I stumbled across this
MSU Video Quality Measurement Tool which appears to be tailor made for this - allowing comparison between source (avs input) and two alternative encodes (avi input).
Has anyone else used this tool? Any advice?