I think pantheon is the equiv of ranked - i dont think custom games add to your rank.
Err, no, I'm pretty sure at this point every single game, even with the other DGs being 100% AI, add to your "rank" (or equivalent thereof in DG). My player sheet in the Pantheon webpage is not empty, even though I have never played Pantheon.
Keep in mind, however, that the ranking system is soon going to be reset anyway after the devs have established what games they would like to have contribute to rankings and what they would like to have not contribute to them.
(They said that they would like only Pantheon games to contribute to rank, as you have assumed. However, I think this is a big mistake unless they make some major changes to Pantheon.)