They're two different ships. Apophis was done by Stratcomm after Inferno R1 came up with the Apothess. AFAIK, they're unrelated, except for the fact that the Apophis was better looking by far (not hard with a lot of the early inferno Vasudan ships), so it got grabbed as a replacement for future releases. Otherwise, there's no connection, and the names are coincidental.
EDIT - Wiki seems to think that Stratcomm's version hasn't used as a replacement for the Inferno ship, and that he may have been inspired by it. Still two separate vessels.