Having just finished both a FD ECM and DBW install, I can help a bit with sorting out the wiring and options.
The FD harness does indeed handle both the ECM and DBW modules all in one harness. Follow the harness to make sure all wires are soldered in - it is possible to only solder in the ones you need for one module or the other.
The bypass connector is a smaller connector with two shorting wires inside it. I can pull my harness for a photo if needed/desired.
There should be two circular rocker switches attached to the harness, or at least two sets of two connectors that are made to connect to the switches. One is for DBW, one is for ECM.
Regarding the use of a used ECM/DBW, the FD modules do not act independent of the installed Maserati ECU and TCU, they interact with them to achieve the desired results. So, the reason they want to code your module to your VIN is to match their modules to the version number of your ECU and TCU. There are some great threads on this forum listing each TCU and ECU version number for each year and model - note that some models change version numbers mid year. In short - I'd just pay FD to make sure it's right if you pick up a used box.
If you want any pictures or assistance, I'm more than happy to assist - the harness and switches are quite easily accessible in a LH drive. I have the switches mounted on the inside of the glovebox.