I think Hello has you on the right track. For you to purchase this boat you should first determine what has compressed and why. Then you will be able to judge whether your shim is a cure or a cough medecine. It would seem to me that Beneteau, by suggesting the shim, feels that it has compressed as much as it can. Now they want you to bow the thinner, compressed section of deck upwards. Could it be that the real solution would be to rebuild that portion of deck from something less compressible? (Thus fixing any potential water intrusion simultaneously.)
Did the compression post actually "sink in" to it's step? If so then shim. If not, fix the real problem.
Oh yeah, ignore all the Beneteau haters. It's not just your boat they hate, it's most boats!