I get some people not liking it, but D&D has fundamentally always dealt with Good and Evil as objectively true things. This means that anybody using those rule systems to create a game needs to at some point attempt to define what sort of action may be Good and what sort of action may be Evil. Since people are different these definitions will never be universally agreed with and that's okay.
This is confusing enough for companies to get across to people without also adding in substantial flaws into the deity. I mean, if Good is objective, but we can't assume that what a Good deity of family stands for in regards to family life is Good, then where does that leave things? If objective Good isn't meant to be judged from the teachings of a deity where is it meant to be judged?
Obviously everybody is going to draw a different line on where a particular action fits on a Good --> Evil scale. But if you're going to work with an objective alignment system then things do belong on that line somewhere. Nobody is going to come around to your house and slap you if you draw that line at a different place from Paizo. But Paizo need to at some point mention what they consider to be objectively Good for their own work to make sense.
That's the thing though.
The gods aren't 100% infallible. They're STILL people. To assume otherwise implies a terrifying level of personality-death. There's Gods who became gods after being mortals (Like Iomedae and Cayden) who are still portrayed as very human. Iomedae's a petty... person, and Cayden argues with his favoured-prostitute-turned-Herald and apparently made his dog immortal.
The gods are already shown to be sentient beings with their own wants and personality quirks, so they don't get to be 1-dimensional non-characters, existing only to show 'this is good' and 'this is bad'
In an objective alignment system, how is Paizo meant to portray that though? Say a deity has positions A, B & C. A is a clearly Good (capital 'G' meaning objectively good) policy. B is a little bit questionable but broadly Good. C isn't Good at all, and could in fact be Evil if people followed the idea through to an extent the deity wouldn't (but may think about). You'll make the teachings of each god broad enough to be effectively useless I think, and something that somebody of any alignment could rightly argue they're fitting into.
A deity can still be a multi-dimensional character and have consistent positions. There's also plenty of potential to suggest that there's a difference between what a good deity may believe and what he or she believes is right to teach followers. In the real world one of the most admirable traits (to my mind) is when people work around the flaws they have to avoid making life worse for other people.
And lets take a step back here. There will be people in the real world who believe that misogyny is a genuinely Good thing, just as there are people in the real world who do not believe that. Some people will honestly believe that purging misogyny from Erastil has actually made him more flawed. So when somebody asks for a deity to have more flaws what does that actually mean when individuals are trying to align their personal moral views into a world where morality has been objectively defined?