Here is a typical example of using the Flexible sub-assembly option:
1. You have an assembly that allows motion of one of the parts (say a slot mate so a bolt can slide within a slot).
2. You want to add the assembly into another assembly and still allow that bolt to move, so you select the Flexible option.
To achieve your goals, with the main assembly open, I would add an in-context "locating sketch" in your PCB assembly. The sketch elements would have coincident relationships to the other parts in the assembly.
Now open the PCB assembly on its own and mate the PCB parts to that "locating sketch".
Later, when the main assembly changes part locations, the PCB locating sketch will update and the PCB parts will also move.