Ok, I finally have the stain I like for our new douglas fir flooring. The problem is, I am concerned that some sort of trowel-able wood filler just won't match well becuase fillers, even the kind you mix with saw dust are notorious for being off color, and very noticeable.

In fact, I over ordered my amount. I will probably be cutting out all knots, and pitching, to get it as clear as possible. Almost all of the wood is VG, and some rift.

So, if I really butt the T&G up properly when stapling, do I really need to use wood filler? I also can't stand that cracking look wood filler seems to inevitably get over time./

I have never trowel filled a wood floor. It will be necessary to fill a few nail holes next to the wall and this can be done before sanding or after the first coat of finish.
You can anticipate the wood will change color over time so color the wood putty a little darker than the color after the first coat of finish. You may be able to find different colors and then mix to match, or color white putty with artist colors ground in oil, or universal tinting colors.
If you use a wood patch before sanding, use the color that will match the wood with a natural finish. Stain will color the wood patch to look like the stained wood color because the density and composition of the wood patch matches the wood close enough to not notice a big difference.
I have seen floors where all of the trowel filled wood filler has not been sanded off thoroughly because the filler matches the raw wood color and when the light changes the color of the wood over time the filler shows up like a ghost. It can ruin the look of a floor.