Instead of a given domain, I can instead take a subdomain. Now, apparently not all deities give alll possible subdomains (unfortunately, Table 2.12 only contains entries for the 'top twenty'), but it appears that I only ever get one aligned outsider subdomain; the one sharing the deity's alignment.
Thus, Asmodeus will grant the devil subdomain, Urgathoa, being NE, allows me to take daemon... while Calistria (who was CN last time I checked) does not grant protean, but rather azata (which clocks in at CG).
Is this intentional? If so, how should I proceed for other deities not belonging to the big 20?
I would go by their portfolios. As an example a god/goddess of love might have the lust domain, if there is one. There is no exact rule for it though.
Is this intentional? If so, how should I proceed for other deities not belonging to the big 20?
In this blog post, James Jacobs talks about the Subdomains for the other deities in Golarion.