What is that putty on windshield pinch weld

The white stuff you are seeing under paint is probably seam sealer.
Just get the metal flange relatively flat as Redfish said. I filled a couple low spots with a smear of JB weld. Seam sealer takes too long to dry.
Factory body manual does call for sealer in both grooves for glass and metal. I like the 1/4 inch black ribbon seal put in the gasket first where it goes on the metal. I put a fine bead of 3m Windo-weld ( caulk gun) under the glass side of gasket lip after its all settled in place. Manual calls for a 3/8 bead of caulk on top of cowl for lower part of gasket to sit in. NAPA has a butyl caulk that works good for that.
As far as actual install procedures, it will vary by gasket. Some have zip lips, others use fill strip or none, or combination...