In 2001 I don't know exactly why would The Blueprint be above The Strokes. In acclaim they are pretty much tied and considered some of the best albums the decade has to offer. They are both popular albums, almost equally, too (if we talk in terms of sales). Blueprint is only x2 Platinum in the US and x1 Platinum in Canada and Gold in UK. Is This It is x1 Platinum in US, UK, Canada and Australia. So that is pretty much a tie. I don't know how influential Jay-Z is, but The Strokes were a huge act in the sound of '00s rock music, specially the Alt. Rock scene. So I still believe Is This It > Blueprint
The editor might be considering popularity for the US and UK only. If so, The Blueprint would win, but not by all that much. Jay-Z is a more influential artist overall, but it's a tougher call when talking abunt just these 2 albums. Pretty close I'd think. Overall, it's definitely closer than the '00 matchup, but I'd say Jay-Z gets a slight edge, and in any event, it's understandable why it would be as it is.
In 2004 I can understand Funeral not being #1, but that doesn't mean it's ok for it to be #6. For example it should be above Smile and Franz Ferdinand. I think it should be #4 at least. And I don't know if this has been discussed, but i think 'Hot Fuss' by The Killers could make a serious case to get a spot somewhere. But I don't really know. I'll have to think more about it.
I could definitely see Funeral ahead of Smile and FF. And it does seem that Hot Fuss is more deserving than some of what made that list. I'd support bumping something, most likely the Black Keys, to make room for it.