I'm probably missing the true point, but to an extent the 622 does keep separate settings for HD and non-HD channels. It does pass SD through at 480, and lets you select HD at either (all) 720 or (all) 1080i. If you use the # key to set an SD (480) channel to Normal, Wide, Partial Zoom, or Zoom, this only applies to the SD (480) channels, and the same is true for the HD channels.
I had a SA8300HD with TW, and did in fact set up native pass through. It was pretty slow changing channels when it had to go from a 720 channel to a 480 channel to 1080i channel, but was fast when it was changing to the same resolution type.
I guess i've gotten a little less picky when it comes to the distinction btwn a 720p and a 1080i channel. For the most part I can't see the difference when I'm watching a 720p show in 1080i mode versus watching it in 720p mode, nor watching a 1080i show in 720p mode versus watching it in 1080i mode.