A couple things going on. First, both Mapper and HEC-GeoRAS create “wse tins” and just apply it to the terrain you provide. The wse tins are based on the cross-sections extents and cover the entire cross-section unless you put a levee feature in the cross-section which it then clips the “tin” to that point.
Second, in the 1D HEC-RAS model, it has no idea if areas should be connected or not. All it does is a calculation based on the shape of your cross-section. This is where understanding limitations of models is important. 2D would more detailed so if you set the model up correctly, it would know if areas should be connected or not.
Not sure what the purpose of your study is for, but if you don’t think water can get to a certain location, I would either put a levee feature there or trim the cross-section shorter. If you are running multiple flows (low and high) where the high flow does get out there, you would have to set the levee elevation just above the low flow wse and below the high flow wse.
If it is for FEMA, they won’t allow a levee feature unless it really is a levee and so you would just have to make it ineffective and then clean it up in GIS.