We're considering #3 common oak for a floor but I have concerns about the durability of the filler for the knots
What is recommended?
Upgrade to a better grade of oak if you plan on filling #3. It will be money well spent. Filler shouldn't be used at all, except in the smaller than a dime sized knots that end up knocking through when installed. Even then, I'd cull rather than fill. You will cull a higher percentage of #3 than it's worth fooling with. Which translates into a much higher price per board foot than just buying the better grade to begin with.
If you like the cabin grade thats fine. For the larger knot holes i simply use epoxy to fill knots. Dries clear sands nicely and you dont have to worry about matching color with filler
I like the idea of epoxy filler! I may try that in a different house.
We looked at our desired timeline and don't have the time to deal with the filling, sanding, staining, etc. So we're going with pre-finished #2 common to match one of the older floors.