I am familiar with fluid volume extraction techniques, but my experience is that for complex assemblies with tens or hundreds of solid bodies, the only way to get the fluid geometry is to use the subtract method. For simple pipelines or one or two complex hollow bodies they are good for internal air/fluid volume, but not for more complex cases.
The problem is that it does not subtract solid bodies from the fluid volume for which the "check geometry" command does not show any errors. I believe this is due to the duplicate surfaces I attached a picture of in my original post. If these were fixed then the problem would be solved and Spaceclaim could subtract the body from the fluid volume.
For some reason I can't fix these duplicate interfaces with the Repair/Duplicates command, but remodeling is not possible because each one has a special unique identifier so it would be a nightmare to remodel them one by one and manually enter their current names. (these unique identifiers needed to define the heat flux boundary conditions in Fluent)