I have never heard of such a thing. As the floor expands/contracts over time the putty would be pushed up above the surface. A definite no-no in my opinion.
Wood filler will not stain the same as the rest of the floor. How big are these cracks that you want to fill? Small spaces between the individual boards are normal as a floor ages, but I'm talking less than 1/32 of an inch.
It sounds to me like you should find another floor finisher.