Its more that the player's civ will just end up conforming to their surroundings despite the flavours of their civ. If you start playing Korea and you have lots of really inviting city sites you're likely going to expand quickly to fill them and not RP and say, well this triple lux river and mountain site here looks good but I'm not the expanding type.
Of course I can't speak for everyone...
This doesn't mean civs shouldn't be designed with their actual history in mind however - how else will the civs be dfferent gameplay wise? From a design standpoint if you don't work with their real world traits you may as well decide on the effects of Unique Assets by rolling dice.
I think that's a consequence that just has to be accepted, honestly. You're right, if you pick Polynesia and end up on a big continent with lots of city sites, you're not going to settle overseas and you may only explore overseas a little bit early on, and then you don't get much use out of your particular benefits. But if they want to make Polynesia play noticeably different on average, they just kind of have to deal with that, I think.