Simon, I agree with you that ultimately it is pointless to compare fighters from different eras for the reasons you've stated.
I also agree that Ali carried on far too long - in the Holmes fight, Angelo Dundee eventually stopped it after round 10 - disgraceful!
'Ali was top in a golden age of HW boxing' - this is the part that I'm still trying to work out.
Ali, though obviously great, benifited from one or two gift decisions. In the 3rd Ken Norton fight, it's hard not to feel sorry for Norton at the end when the judges somehow awarded Ali a unanimous decision. Every close decision of Ali's career went his way.
Ali also got away with a lot of clinching. This is illegal, and if done persistently can alter the course of a fight (such as Ali vs Frazier 2).