Top-level design as (.bdf file) with instantiating CONFIGURATIONs and GENERICSs

If you did all the code in vhdl, then you can use generics to enable or disable blocks at compile time via generics. Fibrous can be passed through from graphical files via block parameters I think, but I don't think bdf files instantiated from vhdl can have generics. I highly suggest you ditch the bdf files and stick only to HDL.