Remove the pan head screws when dry. Then countersink the screw holes to a plug size-ending just short of the plywood, and epoxy in full depth teak plugs. I may need to do that to keep some pieces to a bend, such of the margin pieces that meet the curved plane of the coamings. But I'm thinking I will be able to clamp/weight the decking down, at least on most areas. It will definitely be best to not have any holes.

It sounds like your sole was possibly 'caulked' with black epoxy? Or was it adhered to plywood, caulked with traditional poly sulfide teak caulk, then screwed down?