When you said " no rust - I noticed when the windshield was installed. " I assumed you stood there.... to learn about how the pros do it in case you wanted to DIY sometime....
I don't know the answers to your questions... I just believe in using GOO when installing windshield rubber.... and some people don't....the shop manual specifies using it... and give a part number..... if they had you might not have a leak even with it not tucked in at all the right places... if that is what has happened... but to me the windshield seal should not let the water get to the lower place you describe... if done correctly....