The first sentence on p. 302 seems pretty clear to me: "If you have multiple abilities that give you a focus pool, each one adds 1 Focus Point to your pool." The domain initiate feat says it gives you a focus pool, so the rule on p. 302 applies.
Abilities and sources are not the same thing -- the definition for ability in the glossary even refers to abilities as having different sources, which it wouldn't do if they were the same. If you have two abilities that each give you a focus pool, you get the points from both. Just because it is the same feat doesn't mean it isn't two different abilities. (They are different spells.)
Not that Hero Lab counts as a definitive source, since they have a number of bugs, but they currently give you 2 focus points if you take two domains.
I totally see the argument that Deity's Domain doesn't grant the point because it doesn't say so, and if someone was running a game with that interpretation, I wouldn't complain. (Honestly, if someone ruled that way, I'd probably just spend an extra feat to multi into cleric and then buy the Domain Initiate feat - you could even do that with retraining. Pick the Divine Domain feat at 2, and then at 4 MC to cleric and add Domain Initiate).
I do think they should have been explicit and said "this grants you the spell but not the focus point", so that there's an explicit exception to the sidebar.
Anyway, it is probably not game breaking in either direction. I certainly hope to see a clearer ruling on focus spells (both the cases we've been discussing) in a FAQ.