This is a common complaint, and it'd be nice if there were a different color or some other indication that some of the flights weren't in the selected class of service, but the flip side is that in some cases the TATL is available in the premium cabin and the domestic is not. In those cases you'd want to see the mixed option.

As for getting to CDG from IAH, you shold also be able to see the AF non-stops, I think, online. Certainly you can call and ask about them. From NYC there is a ton of availablity on AF these days. You might even be able to do IAH-JFK-CDG with the TATL on AF. Of course, getting a seat up front on the 735 from IAH-JFK may prove to be difficult, but like you said, the TATL is the important flight. Also look at other AF gateways, such as ATL or ORD. Tons of options with only one stop to CDG, but most of them aren't online.