To me you do not get a second focus point from taking Domain Initiate. Reading the entire entry
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Domain Initiate
Your deity bestows a special spell related to their powers. Select one domain—a subject of particular interest to you within your religion—from your deity’s list. You gain an initial domain spell for that domain, a spell unique to the domain and not available to other clerics. Each domain’s theme and domain spells can be found here.
Domain spells are a type of focus spell. It costs 1 Focus Point to cast a focus spell, and you start with a focus pool of 1 Focus Point. You refill your focus pool during your daily preparations, and you can regain 1 Focus Point by spending 10 minutes using the Refocus activity to pray to your deity or do service toward their causes.
Focus spells are automatically heightened to half your level rounded up. Focus spells don’t require spell slots, nor can you cast them using spell slots. Certain feats can give you more focus spells and increase the size of your focus pool, though your focus pool can never hold more than 3 Focus Points. The full rules for focus spells appear on page 300.
Special You can select this feat multiple times, selecting a different domain each time and gaining its domain spell.
In the Special disclaimer it says you can take this feat multiple times however only receiving the spell from the alternate domain selected. There is nothing about gaining an extra focus point.
In addition it says in the second paragraph that you start with a focus pool of 1, doesn't say add a focus point.
Look at Lingering Performance from the Bard feats.
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Lingering Performance
Prerequisites maestro muse, focus pool
By adding a flourish, you make your compositions last longer. You learn the lingering composition focus spell. Increase the number of Focus Points in your focus pool by 1.
This specifically says increase your focus pool by 1. A non-archtyped cleric has very few opportunites to add to their focus pool.