Stain and finish the floor, then use matching filler.

You can even blend the available colors to get a better match.

I may differ with brickeye here. If you are referring to a custom floor then fill the floor first, prior to the final sanding. Your glue- fine sand dust method will work but is more tedious than an off the shelve product.
If it is a prefinished then I would fill last with a precolored filler. Keep in mind most have an oil base that needs all the residue cleaned so not to leave smears on the surface that attract dust. The glue version would be much more trouble to clean up, stain and seal.

"If you are referring to a custom floor then fill the floor first"

And then every single repair spot is going to show since pigment stains (normally used on floors) do not take to sawdust & glue filler anything like actual wood.

Sawdust and hide glue filler is used with aniline dye since it takes the dye very close to solid wood (at least for the water soluble aniline dye).

Paste filler for large scale grain filling is tinted also so it will blend with the final color.

You can use contrasting paste wood filler for certain decorative effects, but be aware it does NOT take ANY stain or dye like solid wood.