Schematic Design and Non-PCB Mounted Components
I am not a professional PCB designer.

My rule is: put all the connected electronics on the schematic. 

The chassis-mounted parts need nets for their connections, otherwise what will they connect to? The simplest way to achieve this is put the chassis-mounted parts on the schematic.

The chassis-mount parts will need a PCB footprint for the connecting wires. So I design that footprint (set of holes) for the PCB, and it is self-consistent; the PCB is constrained to support the schematic.

Further, the PCB footprint can have a silkscreen label, showing how to wire it to the chassis-mount parts. 

Also, I can generate an assembly guide from similar information.

I can derive the Bill-of-Material from the schematic, and I have less chance of forgetting something. I don't need to look in two places to know what the circuit will be.