Say I have a part that can come in two different forms, with different footprints, or alternate devices that fulfil the same function in the circuit but have different footprints.
I want to inlude BOTH footprints on the board connected approp[riately by traces, but only one will be populated at any one time. This is to give the person building the circuit the choice of parts.
what’s the best way to do this?
I could draw a schematic showing two devices in parallel both connected, but that would be misleading and wrong.
That’s a good question I still don’t have a good idea how to make this possible. I also didn’t see a good solution in other EDA tools yet. I think usually the workaround is still to add both devices to the schematic, place the footprints overlapping and suppress the possibly appearing DRC warnings 
The simple way to make this possible would be to allow adding devices and traces directly in the PCB editor that are not on the schematic. Sure this would allow people to make a mess - but it would also allow a lot of tricky uses without excessive overhead, and no-one has to use it if they don’t want to.
The extra devices could perhaps be displayed with the placement layer tinted a different colour so it is easy to see which components are on the schematic or not.
This would allow a wide variety of use cases, including making a quick simple pcb without using a schematic at all.