I think you would be OK doing that. I think I did that also, but can't remember. I did put a small amount of sealant inside the rubber window channel before installing the glass- but not enough to seep out onto the window when glass was inserted in the rubber. I did not put any sealant on the inside surface edge of the 1/4 window garnish molding so as to make it easier to remove the garnish molding later on, if needed. I didn't want it sticking to the glass. The reason I put the "bead" on the outside (on my first post) was also because I didn't like the appearance of the space between the outside body and the glass. It just seemed logical to seal it for the sake of appearance and potential leakage. If you are restoring a 100 point car check to see how it was done at the factory as I am not an expert restorer.