I don’t think a lid is treated any differently than any other change in the cross section. For instance, if XS-3 has a channel that is 100 feet wide, XS-2 has a channel that is 50 feet wide and XS-1 has a channel that is 100 feet wide.
Depending on whether you are doing steady or unsteady flow and user options: There will be a velocity that is computed at each of the 3 cross sections. It will compute a contraction and expansion loss using these velocities. Using Manning’s equation, there will be a friction slope at each of the three cross sections. And from that, friction losses are computed depending on the friction method that is selected.
So RAS isn’t really assuming how wide the deck is. But to answer one of your questions, if the water hits the lid at XS-2, it will affect the computed losses from both XS-1 to XS-2 and XS-2 to XS-3.
I guess as a rule-of-thumb approximation, you could think of it extending halfway from XS-1 to XS-2 and XS-2 to XS-3. And if you wanted to more explicitly define the limits of the deck, you could interpolate additional cross sections and choose which ones to attach the lid to.
If you want to dig into it, the RAS Hydraulic manual has quite a bit of info.