Wood expands and contracts with changes in humidity. It changes most across the width of a board, up to 8-10%, and least along the length. The only way to stop this natural process is to keep the wood at a constant humidity level before, during and after construction of a floor. Tongue and groove joints allow for this movement and you will note that you only nail one side of a tongue and groove floor to allow for it. Wide boards show gaps between themselves more than narrow boards. The total change is the same but the gaps are broken up into smaller segments. That's the reason why 2-1/2" wide oak T&G is the most common hardwood floor.
If you fill the gaps between the boards, the process does not stop. While there can be some "squeeze-out" of the filler, but what normally happens is that the wood fibers next to the filler crush with an increase in humidity. When the fibers crush and then contract with a decrease in humidity, they leave gaps. Eventually, the gaps will be the same as if you had not put in filler. This may take several years but it will happen.
Floor finishes can slow the process of the wood absorbing water vapor but not stop it. Finishes vary in their ability to slow the water vapor exchange rate but film thickness is a big part of the equasion of how fast this takes place. However to be effective, you have to slow the exchange rate by finishing all 6 sides of a board. Engineered wood floors move too but that is why they have to float and allow a gap around the perimeter.
So the bottom line is that you should not apply a filler between the cracks. Several coats of an oil based poly will slow the expansion and contraction a little. A good subfloor helps too but only if you have something to slow the water vapor exchange. And one other point, no filler accepts stain the same way real wood does.
Good luck and post back if you have any questions.