You appear to have already used the pier function, so that area is removed by HEC-RAS from the perpendicular flow area that it reports on the Bridge tab. When you put your piers in, remember to reduce the span by the skew angle. Typically bridge engineers will place a longer span over the main channel. Personally, I place as many piers in the flood plain as needed in HEC-RAS and let the bridge engineer determine the configuration.
When you pass the perpendicular flow area to the bridge engineer, you have to add back in the area removed by piers (# piers x pier width x depth of water). Around here, the bridge designer has to provide the perpendicular clear area under the "natural" 100-year elevation (i.e. no bridges). We therefore add back in/remove the area of water above/below that elevation under the bridge (top width x elevation difference). We compare the elevation on the Bridge Table to the natural elevation linearly interpolated at the downstream face of bridge station.
You appear to be using the upstream and downstream cross-sections for your internal bridge x-sections. (This is the HEC-RAS default.) I will cut a cross-section under the bridge at the exact location the bridge engineer will be using. If you look at your exhibit, the cross-sections are quite different, and different again to what the bridge engineer will use. Using the actual bridge location internal x-section and properly adding back in pier and water surface elevation difference areas means that your bridge engineer shouldn't have to provide compensatory grading.
I wouldn't necessarily bother to put obstruction in the cross-sections because the abutments are within the expansion and contraction reaches and will be inside ineffective flow areas, and therefore already blocked out from the flow area by HEC-RAS. The bridge engineer should design the deck to be a trapezoid rather than a rectangle, with end bents and abutments parallel to the flow direction. (Like
this.)
You absolutely MUST leave scour protection up to someone who understands it and is experienced with it. Grouted riprap is very BAD for scour protection. There are a number of NCHRP documents on bridge scour (prompted by bridge failures with loss of life) and some outstanding classes.
This book will be a useful start.
This one explains scour countermeasures.
Here regardless of apparent channel stability we provide pier scour protection to the depth required if the pier were in the channel. Channel migration does occur, usually when you least expect it. In a live bed situation (where scour holes are filled on the down leg of the flood hydrograph) visual scour monitoring after a flood is useless.
WRT who to discuss your modeling approach with, I'd pick whichever of the FEMA person and the floodplain admin you have the better relationship with/who will sign-off on the model. Hydraulics is usually on the critical path, and nobody likes it when the reviewer makes you redo your model. (Fortunately I was the one redoing other people's models.)