The only explanation I've ever been able to come up with besides carelessness to explain why some Hulu transfers are better then what we got on DVD is the fire.
They perhaps used what was readily available on hand rather then doing new transfers for the DVD release. And after the fire and the release of season 4, they perhaps went back to the original prints or better source material and made new transfers that were actually superior to what we saw on DVD when they started to rebuild and replace destroyed material? So now they have superior transfers of some of these episodes that simply weren't available at the time for the DVD that we've seen become available digitally.
We're basically faced with hoping for a complete series release and an opportunity to double dip if we want to escape the double sided disc of the earlier seasons (Especially the season 1 release) and get the superior transfers for particular episodes that they're now using for digital delivery services.




