No, there is no means for users to add custom FPGA logic to the RT Box. All FPGA functionality is configured by the RT Box library components included in a model and the code generation settings.
Can you elaborate what kind of functionality you’d like to implement and what input data you’d like to use? Also, we’d be interested to know if you intend to write VHDL / Verilog code yourself or if you intend to use another toolchain.