Thanks again to all for their suggestions. Each method worked better than what I was doing. What I had started with were the flooring boards in the cabin, because I needed access to some nuts that came thru the hull planks (it's what they call double planked, one row of real planks over the top of plywood, and of course the plywood is what is giving me problems due to former owner not caulking the planks correctly).
Once I removed the thru bolts, it was clear there were many screws that were fastened to these cross members from the planks outside (I thought the planks were only fastened to the main cross members, these are just some braces.
Bottom line is the best solution on the underside of the hull was to use my gasket hole punches. One or two whacks would get the whole plug including most if not all of what was in the slot. However these were mostly silicon caulk plugs rather than the wood putty plugs above decks. (In regards to the point regarding wood plugs, I have found that those tend to only be used in visible areas such as the teak decking, and mahogeny deck surround).
Something that dawned on me towards the end was to try chucking the punch into my drill. Unfortunately the drills I had at the boatyard were all 3/8" and it would have taken a 1/2" chuck to accept the size punch I was using. If I find I need to continue this removal process I may try that out.
Bottom line for anyone who bumps into this thread in the future, I'd try the punch method first. Harbor Freight (or Horrible Fright depending on your outlook on cheap tools) sells these for $5
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somewhat of an aside, there were a couple of screws that were "stripped" due to dry rot, so although the head was intact, they would not back out, and it was difficult to get a pick behind the head to help it along. I finally decided to try my "Grabit" screw removal set. I was very amazed and please with the results. First you burnish the screw with one end which obliterates the screw slots. In one case the screw came out with just the burnishing tool which is pretty much a backward drill bit head. Then you reverse the bit and the thing really grabs onto the screw and pulls in out. One caveat, these were all brass screws, so your mileage may vary with other types of screws.
I've used this group many times in the past just by using search, so I've not had the opportunity to say thanks, so regulars, please accept this as a thanks for past information as well.