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Some water based fillers do a pretty good job at filling smaller cracks...but it appears here that some of these are quite a bit bigger. Considering the height variations a tooled in filler will leave many "corners" of filler., if it is filled before a rough sanding is completed....even then you will still have some.
A Good quality sanding along with a good refinish job will make the floors look really great. Even with the gaps and spaces. This is the charm of the older floors. Many new flooring systems try to mimic that very look. So your way ahead of the trend.
However if you really want to loose the gaps, you need to hire a high end flooring company that can remove the floor and re-salvage the wood. Then simply re-nail it back down and add a new course or two of boards so the joints and spaces are tight again. Then when done refinish once more.