It is possible to map the pins differently for each footprint, but I only do it for generic parts like transistors or voltage regulators. It's least confusing to use letters to label the pins (D, G, S for a MOSFET) and then use the Pin Map to assign it to numbered pins for each footprint. You can find the Pin Map button in the dialog where you select the footprint, after clicking "Edit" in the schematic library or properties of a placed symbol. But then you have cases like nets that are on more than one pin (SO-8 MOSFETS) and you end up needing a separate symbol anyway so you can have 3 pins on top of each other so they all get electrically connected.
For ICs I just use separate symbols always, and use the manufacturer part code to name the symbol so it matches up with the BOM.
To answer your question more literally, even if the pinning were the same I would only put the one footprint I'm using on the symbol because any "extra" work I do is work that I'm not going to bother checking, and then 6 months from now I'll rely on it and get screwed because I chose the wrong footprint.