Oh BTW I didn't actually try Instapaper w/ Calibre, just by itself
I have done a side-by-side comparison now, and here are what I see as the pros and cons.
Fetching Intapaper feed with Calibre:
+ Preserves all comments
- Atrocious formatting in ePub
- Aspect ratio of some images not maintained
Creating ePub from Instapaper:
+ Beautiful formatting
- Blog comments not included in ePub
Note that I haven't attempted to finesse the Calibre news feed formatting at all. I just added my Instapaper feed and fetched it.
But for my money (that would be zero dollars!) Instapaper does a better job or ePub creation. If there was an option to maintain comments then I think it would be perfect!