He is only using those as he fits the pieces together... the screws ensure that the spacing comes right every time and the oversize head pushes the wood all the way down to the surface below... especially important during the epoxy glue phase.
He will eventually remove all those "temporary working screws" and put in recessed screws with proper fitted bungs and then sand the whole affair down as one unit to finish it.
Lots and lots of tiny details are going into this that folks like myself are not even aware of when we look at a proper deck.
Thanks Tom for this lesson in fine wood wood and boat details... keep it going... ahhh the lessons we're learning.