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The top picture is closer to correct. the second picture someone has welded in a cap or patch. this spot is where the a pillar, upper inner windshield frame and outer windshield frame prices come together. the gasket for the doors would screw into the three pieces with those flat head Philips screws. I welded up/created a bolt on header piece that covers all of that for my soft top. that way I could have a flat metal surface to mount my window frames to. I'm in the process of getting my soft top on and can snap some pics for you in the next couple of days.
Here is a link to one of the only kits on the market to recreate the whole top piece: