I would recommend you try a project box setup for both if you can’t fit the PCBs inside the case. My reasoning is this: It sounds like you’re going to be doing the work of putting the boards in a project box anyways. If you make them both project boxes connected to the UPCB 15 pin dsub, you can easily drill a little hole in the 360 project box for a Guide button switch. Trying to go the route you described will be one hell of a lot more work that you have to go through. The d-sub connectors will be a ton larger, a whole 'nother one will have to mounted on the case and wired up, and the wiring of the pads will be more work since you’d have to remove the cable, solder the cable to a 15 pin d-sub, wires the spots for the cable on the PCB to the 25 pin d-sub, etc.
As long as you put in a button on the box for guide, you would also gain all of the functionality of the guide button, such as turbo and button remapping. If you went the way you described, these options would not be available to you.
Now, if you still want to go with adding another 25 pin d-sub, the way you describe it will work, but only for one piggybacked system. Each system has two pins it communicates over: DC_1, DC_2, X360_1, and X360_2. You have to make sure those four pins are present on your 25 pin connector. When the UPCB sees a piggybacked DC cable, it will connect the DC_1 and DC_2 pins to the cable; ditto for Xbox360 and the X360 pins. There is also the XBOX_PB_SELECT and DC_PB_SELECT lines; you can skip those or keep them if you like, they would not be required. That leaves 17 pins for all of the buttons, directions, etc, and those are all shared between both of the PB connectors. All of those have to go to your box.