My understanding of it is that the topical pour-on works best for external parasites such as mites, and the injectable given orally or subcutaneously works best for internal parasites.
Giving it orally causes it to be absorbed more quickly and reach a higher concentration in the bloodstream, while with injection is absorbed more slowly and takes longer to leave the bloodstream.
I always administer it orally unless I suspect a very heavy wormload. This could cause too rapid a die off and risk developing anemia or even enterotoxemia from all the dead worms in the gut.