We too use automotive filler in vast quantities and it had been fantastic to fill large gaps in the timber floors. It doesn't pop out, sands and varnishes well with anything, but.... it isn't a great colour, in fact it is pinkish too. I wouldn't use it over a whole gappy floor because it would probably stick all the boards together preventing necessary movement, and it might look a bit odd due to the colour. I recall the first really cold night after doing our floors being woken to these exteremely loud cracking and snapping sounds. It was the floorboards breaking apart where the 2-pack varnish had 'glued' them, due to the shrinking effects of the cold air. Nothing visible to the eye though.
If I were you, and liking the look of the old boards, I would consider fixing some ply or fibre cement sheeting to the undersides of the boards between the joists to stop the air movement and leave the top, gaps and all. You'd keep the rustic looking floor and make it airtight. This is assuming you can get to the undersides of the boards though.
