No, for all the problems with the hood on ours (well basically one single problem that they just couldn't fix), being watertight was never a problem! When the roof closed, it closed with a tight seal and we never had any problem with water getting in, even parked outside all the time in all weathers. When the roof went up, it would sort of 'tighten up' right at the end of the process, you could see it basically finish the process then pull itself taught.
Sounds like you're being told a bunch of BS - sadly, in my experience, I have to say that *is* typical customer service from Alfa dealers. And I wouldn't put much faith in the Alfa technical reps either - we had them sent out to dealers 3 times and each time they failed to fix the problem. In one case, he flat out told me the motors that had been sent weren't up to the job and would keep failing (which, to be fair to him, proved to be exactly right!).
Having said all of that, don't take any flannel, insist they refit it - correctly. And with a bit of luck once it's sorted it won't cause any more grief, it should certainly be watertight. Good luck!