Boyd, if you take a painted piece of metal and bend it to a sharp corner, the paint will flake off. That is the same thing that will happen if you apply any kind of paint, poly, etc. over the wood. Certainly, some caulks are paintable and some dry harder than others, but they have to remain somewhat flexible to work. That's why I think that the caulk is going to be a problem. I think that you would be better off filling small areas with a filler that hardens, like the 2 part Minwax filler, if you have to use a filler at all. If the wood does expand and mashes the wood just where the filler is, that should not be much of a problem. You just don't want to do the whole floor with it. Staining the filler to match the floor wood can be tough but you should be able to get it close.
Poly comes in clear. The water based tends to be somewhat milky looking even when dry. It depends on how the light hits it. The oil based will add an amber cast.