Which connection are you talking about? What is connected to what?
Do you mean that you want to replace the USB-C cable connection between the Librem 5 and the NexDock … with a USB-C dock connector (male) directly coming out of the NexDock (potentially internal)?
Sounds doable (for a dock that is purpose-built for the Librem 5).
I don’t know that you want to use the phone as the touchpad because the NexDock screen is a touch screen anyway. So maybe only mouse click (and scroll?) functions are needed. Some users are complaining about resting their palms when using the keyboard and accidentally activating the touchpad (or in your scenario activating the Librem 5), however that should be solvable.
Still, that too sounds doable.