Now you can edit built-in receipts in calibre.
Subscription uses http://www.nytimes.com/pages/todayspaper/index.html
The other one is from mobile version, http://mobile.nytimes.com
Sites are organized differently, hence different versions of feeds. The mobile version doesn't have "Front Page", how are you comparing articles?
Size of the second version is much larger because it covers most of the sections, while the subscription doesn't have Travel, Auto, Arts, etc.
I'll try to build something in between, to get the subscription version plus few missing sections.