He has taken Practiced Spellcaster in both classes.
Would you reach the same conclusion if the caster levels applied to more than one spell? Say, for instance, if a domain gave you +1 caster level to a class of spell (such as healing, good, etc.)? What if the Arcane Thesis spell has that descriptor (say, this character choosing Summon Monster III, having the Good domain, and summoning a good creature)?
Can you think of any case where it should not stack? I have been allowing it to stack in all cases, since it is not a "named bonus"; I just want to make sure that I am not giving more power to this character than he should have.