I'd suggest mixing up some epoxy in a cup and adding sawdust from the same
kind of wood until the mixture is pretty stiff - it should stand up in peaks
and droop slowly if at all.
It'll still sag some while it's curing, so all you need to do to keep it in
shape is to make some of what used to called "dams": take a couple pieces of
scrap wood, cover them with a strip of smooth tape, and then wipe a thin
film of white grease on the tape so it'll release after the cure.
Do the knots one at a time. Fill the voids with a spatula, tool it until
it's a bit proud all around. Clamp a piece to the underside face and another
to the vertical edge to keep the stuff from drooping out of the patch.
Finally wipe off the squeezed-out mixture and tool the upper face until it's
just very slightly proud (epoxy doesn't shrink to any appreciable extent).
Work reasonably quickly.
After a while, while it's still just a bit green (not yet cured rock-hard),
pop off the dams, give the edge and the underside face a wipe with a small
bit of paint thinner to remove any trace of the grease, and block-sand as
necessary with a coarse paper like 60 or 80 grit to make it flush. Let it
finish curing, and then go over the faces and the edge with finer grits
until you like the look.
The filler will come out darker than you expect, so do a test on a piece of
scrap to see if it's to your taste. If not, there are other special-purpose
fillers for epoxy which come out white or gray, and then you can take a
brown sharpie and just draw over the patches to try to match the grain, or
stain it to suit yourself.
For something like this, I use West Epoxy. You can get different catalysts
which cure at different speeds. For this I'd use slow catalyst so that I'd
have plenty of time to work the patch before it started to stiffen up.
Hardware store epoxy might not give you that flexibility.