You are combining two separate issues.
Firstly, the Fox Sports/Youtube TV issues: When Disney bought Fox last year, one of the conditions of the sale was that Disney could not keep the Fox's Regional Sports Networks (RSNs). So, Disney sold most all of the Fox RSNs to Sinclair. When Youtube TV's contract came up for renewal, they were no longer negotiating with Fox (with whom they made the original carriage agreement, which included the Fox RSNs like Prime Ticket and Fox Sports West), but instead negotiating with Sinclair who now owns those channels. Youtube TV did not want to agree to pay the price increase that Sinclair was demanding for the carriage agreement, so Youtube TV dropped those channels. (Youtube TV originally removed the channels when they went into negotiations, then brought them back while negotiations were ongoing, and finally when the negotiations were completed, some RSNs were permanently removed.)
The second issue you are seeing is a discrepancy between what channels you may receive directly from your cable and/or OTT provider, and which channels you can receive with TV Everywhere credentials. Just as with the carriage agreement between Youtube TV and Sinclair, there is a separate agreement that cable/OTT providers need in order to provide access to TV Everywhere feeds. So, you may receive WarnerMedia channels (such as CNN, TBS, TNT, etc.) through Youtube TV, but you do not receive them through TV Everywhere; you can watch CNN in Youtube TV's app, but you cannot watch CNN in their app or through TV Everywhere. The inability to use TV Everywhere to view some channels that you have access to through your OTT provider's app (ie, from YTTV's app), but not the channel's app (ie, in CNN Go), has nothing to do with Channels. The discrepancy is a result of your provider (ie, YTTV) not paying the networks extra to enable TV Everywhere access.
While Channels' beta support for integrating TV Everywhere streams is quite awesome and usually just works, it is at the mercy of third-parties working together to make it work. Problems like YTTV's loss of Fox RSNs, or inability to authenticate for channels that you can receive through you cable subscription via TV Everywhere, have nothing to do with Channels, and everything to do your cable/OTT provider.