I have never seen the type of damage/flexing you are referring too so I can't comment on whether it is normal or make a recommendation. However, normal settling/flexing should not cause paint to crack or chip. The seals generally do a very good job, it will be watertight in rain. But if you spray medium/high pressure water at or toward the seals during a car wash you can get some coming in near the lock pins, normally not a lot, and it rarely gets past the area already covered by the convertible top drains.
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1999 Ocean Blue Metallic Boxster - blueboxster.com
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