You are correct that it's not necessary to take flats without filters. After taking flats for all filters and creating Master flats for each L, R, G, & B, overlay all Master LRGB flats and you can determine which dust motes are from the filters or CCD window. If the dust motes overlay perfectly for all LRGB flats, then these dust motes are from CCD window. The rest of the dust motes are from the filters.
Peter