My car (a 1989 Subaru XT6) has flush door handles as well, but it is accomplished simply by having a spring-loaded plate swing out and take up the space under the door handle. When opening the door, this is simply pushed out of the way with the fingertips and the rest of the door handle operates like any other. It looks baffling, but it's not hard to use once you have done it or seen it done. The other controls in the car are similar, it seems like almost every accessory is moved to a strange place. Heat and A/C? The switch is on the center of the dash, but the mixing lever and fan speed controls are are on the center console next to the parking brake. The window controls are oddly placed, though they are on the door. They are neither at a relaxed-arm distance nor a fully-extended distance, but right in between, forcing the user to hunt for them. The intent may have been to make them hard to hit accidentally, but it hampers usability (again, until you get used to it). The one that threw me when I first got the car is the release for the fuel door. Next to the seat, there is just one lever. Pulling it pops the trunk, but pushing down on it pops the fuel door. The headlight controls are also very wacky, which can be quite amusing when parking valets are involved.
I have to figure some of these stem from the fact that this car was ahead of the curve on a lot of these things, before de facto standards had really emerged. However, despite all the weirdness, the door handle solution is one that would work perfectly well today on the Model S.