Man, can of worms.
If you want to set the DVR at one rez only, you need to know what resolutions your display best accepts for scaling/deinterlacing. In my case, I know my display is good at both, so I have the HR44 set to Native.
Most 1080p displays nowadays will do fine with 720p/1080i in and you wont see anything. As far as which is better in the same perfect situation, that isnt worth worrying about. Once again, how you set your box output should rely heavily on the performance of your display.
Some displays overscan ALL the time on 720p, and do not allow for 1:1 pixel mapping. That is effectively zooming. In that case, id send 1080i out all the time and let the display handle it to 1080p.
As far as broadcast 720p (ABC) vs 1080i (CBS), sometimes ABC looks good, sometimes it looks like crap. Same with CBS. How it is filmed or shot is out of your control so I would not even worry about that aspect of it.