Actually I don't do this. I do try to keep the filters clean though to avoid dust donuts. The vingetting is very similar between the three colour filters. I have a set of flats for the L at both 1x1 and 2x2 binning, colour at 2x2.
I do need to take a set for the Ha filter as the focus is different.
Even so it's really not that much trouble as once your set and focussed it's just a matter of setting up an automated run for each filter in CCDSoft at twilight. If you keep your filters clean then the camera orientation doesn't matter either (at least in mine).
I do have a light box so I don't need twilight and reading up in maxim shows that it marks the FITs headers as to what each shot is so it should be a no brainer to combine everything, however, at the moment the camera rotation can change night to night which may preclude me from building a library. I still have adapters coming in from the UK to sort that out.
If you don't have any dust donuts from filters etc., then you could just build a library. Use CCDSoft to make flat masters for each filter. Try rotating the camera for one filter to see if the vingetting changes.
As you have a lightbox, just take them after your imaging run.