I have searched and searched but can't really nail down a definitive answer as to how the windshield hinge seal is supposed to go.
Well Mark, as you see this is one of those with no definitive answer. So looking for one (at least for now) is a study in futility.
I used to argue for the rear facing bulb, or bead, because that's how 99% of the ones I'd seen over the years were delivered from the factory. But as has been documented several times over the years here, especially recently by original owners of Broncos, some were delivered from Ford with the bead facing forward, nearest the hinge.
Unfortunately (for me at least) both positions make some sense.
I still install all of mine with the bead to the rear, even though I'd certainly like to keep water from getting into that cavity completely. But since it's open to the sides anyway, I say any position that best keeps water out of the rear area and passenger compartment behind the dash is the best practice. Whatever you can do to avoid water getting inside is a good thing.
Besides, when I first tried putting one back in with bead forward, knowing it had come with the bead facing the rear originally, the frame just did not want to lay back towards the top and doors naturally and I did not want to put that much pressure on things, as was mentioned earlier. So I re-installed it the way it had come out.
First one was on an original 2-owner '72 that had never had the hard top removed (was only two years old at the time). Second one was on my '71 that had never had the hard top removed (was five years old at the time). The third was a '66 with no verifiable ownership or hard top removal history and I was only involved in what appeared to be the first time the windshield had been flipped forward. The other '66 had the flat seal, but this one had the bulb/bead feature.
All those were my own experiences though. At least some of the current owners that have found the bead towards the hinge are original owners (two of them '77's if I remember?) and so know the history of top removal and windshield frame laying down.
Seems like we had someone post up a picture of their never-molested hinge seal with the bead forward.
So basically use what works and what you like, but take some time to fiddle.
In your case that sounds like a non-starter, since it's already done. I'd do the same thing you're saying. Leave it and watch for leaks inside and even for water draining out from between the hinge halves to the sides if you can see it.
Agree it's fixable, but I know it's a pain if you're not already removing your hard top. I don't look forward to that as just a "maintenance" item.
If it wasn't such a semi-permanent fix, I'd just goop the area with silicone sealer until it oozed out of the exposed edge of the hinge. In fact I still might!
Paul