I notice that these two channels and their other affiliated channels are only coming in as 29.97 fps which gives them a slightly stutter look. Is that the best stream they supply to TVE customers? The same channels on the YTTV app look much better.

Yes, Channels always retrieves the best quality stream available, I believe. Although I’m not sure if this is automatic or something in the configuration for each channel that might need to be updated occasionally by the Devs.

Apples and oranges. Channels sources the feeds from the networks' websites; YTTV (or whichever OTT/cable service you use) gets their (higher quality/better/different) feeds from the network directly (read, not their public website).

Just because you use your YTTV credentials to get the feed, that does not mean it is the same feed as you get in the app.