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I wish this was true for me. I've had the car to the dealer and they say nothing is wrong, however, when the top is down at high speeds (>55 mph) the car definitely has a larger amount of body flex than when the top is up. There are other threads on CL that also describe this issue, so it's not just my car. But I can say it is much improved with the coilovers.
I've had coilovers for so long I can't remember how it felt stock. But I'm going to agree with the dealer that there's probably nothing wrong with your car. It does have more structural rigidity with the top up. This is true of any convertible, particularly a hard top.