Yea – but there are enough other diagnostic features (colours, spots, borders etc) that characterize each species that clearly aid identification in most cases - otherwise butterfly guides would be redundant.
For general interest:
Identification of a species by its genitals is a useful tool for accurately identifying closely related species. Today I believe they also use molecular analysis.
Male and female genitalia must fit together (like a lock and key) in order for effective mating to take place. Each butterfly species has genitalia that are unique in shape and form so it is one of the most reliable ways of establishing the identity of a species.
Butterflies that are affected by weather and climate changes, like those in the family Pieridae, have wet and dry season forms (wsf) and (dsf) that can differ so radically in colour that they look like different species. They caused much confusion in the early days and many were initially identified as different species (differences especially true of the females). I wouldn’t be surprised if they used this method to finally sort them out.
The gaudy commodore - Precis octavia sesamus (subfamily Nymphalinae) illustrates how radically different wsf and dsf forms can be.
Not very good specimens but they give the idea. They are actually stunning butterflies.
Hope this isn't too much info!