You need to read up on culvert hydraulics and how RAS displays results. First off everything matters for the final results. A different terrain, BC, flow etc.
Second water is NOT flowing through the lid (or what you call barrier). Water is hitting the face of the culvert (tunnel) and dipping down and is under pressurized flow. The line you are looking at that looks like it is “flowing through the barrier” has a clear label in the RAS legend…Please realize what you are saying before you say it…the energy grade line does not mean water is flowing through at that level…please look into basic hydraulic computations and head.
You need to verify that piessman slots. If you do not know what piessman slots are then look it up.
WHEN HEC-RAS is OPEN HIT F1 people!!!!!!!!