I hear what you are saying but left 'unchecked' a driver with a preference for something will lead development in a certain direction. It's only natural. Please note that I am not blaming FA for Ferrari's development woes as they have developed what's good for him (albeit not overall as fast a car as anoyone would like). Also, my use of unchecked is purely for ease of explanation. Ferrari should have no reason to 'check' their number 1 driver.
No doubt if Ferrari listened to Kimi for 4 years you would have a car that FA would step into and struggle to drive as well as the incumbent no 1 (this is probably akin to heresy to some here who would insist that FA would just 'adapt')
There have been drivers in F1 who have found that they are especially good at dealing with a trait of a car that other drivers cannot handle. The temptation for such a driver to keep that trait is very real, especially if they feel it's gaining them time. For the team it really depends on whether the development direction "steered" by the driver results in an ultimately faster car, at least in that drivers hands. Obviously, the only drivers with a chance of pulling this off are established #1s with a lot of credibility within the team, which knows they will deliver if the car is on the pace.
Schumacher was definitely this kind of a driver. While he could drive a classic "well-balanced" car very quickly, he could also handle cars that felt very strange for others. When Berger and Alesi succeeded him at Benneton they found the car very difficult to drive. His teammates at Ferrari found the cars there (again by Brawn & Byrne) difficult to drive at times too. When the car was more "normal" then Barrichello was far closer to Schumi than at other times.
Alonso seems to be this type of driver too. Whatever this year's Ferrari is doing that Kimi can't handle, he seems to be able to manage. It makes me wonder whether it's a side effect of something else that Fernando wants from the car that the team is giving him. Not that there is anything wrong with that, mind you. For all we know having this "quirk" is gaining them a few tenths over ironing it out to a more "normal" feeling car.
Vettel's ability to master the exhaust blown Red Bull is another example. Had both drivers struggled they might have tried to "smooth out" the way that downforce was applied, but since the lead driver found it beneficial it was probably amplified rather than softened. Again, nothing wrong with that if there's performance to be had.