I'd hope that Seafaring would check for coastal as one of the modifiers.
I imagine you see traits more coming into things like:
Lustful/chaste being more/less likely to allow concubines or polygamy
Zealous/cynical being more likely to pick dogmatic/cosmopolitan
Religions generally being more likely to pick their "unique" reform
and so on and so forth. I'd hope that the more unusual religious traits would be extremely rare anyway.
I don't doubt that there are some things that are weighted very well, but I would suspect that there are possible cases that could spring up where I (or someone else, for that matter) would feel that the decision is subjecitvely wrong and immersion-breaking (for a given value of immersion; I'll still opt into supernatural stuff and Aztecs...).
Sure, you could mod those things out (unless the system is far less flexible than we've been told), but a game rule would make things easier if you want to play a vanilla game to test other things out without having to worry about some pagan ruining the campaign for you with a choice you find to be just plain wrong (particularly if you're playing an Ironman game and thus can't edit the save to deal with the AI's bad choices).