for little holes, especially flat one on deck, those pre-mix glue tubes are very handy. But for anything bigger than 1/4", I use empty caulk tubes and fill using epoxy/filler mix.
With an empty caulk tube, you can fill it with a VERY thick glue. The epoxy glue products that mix within the tip can only be so thick or they will not be able to squeeze through the mixing tip. If you fill the tube yourself, you can make the epoxy putty thick enough to stick on the ceiling
below are 1-1/2" holes filled this way. The holes were pre-wet out with un-thickend epoxy (soaked into wood a bit), then I filled the holes with the putty dispensed from a caulk tube. Putty was thick enough I could put it to the back of the hole (backside of hole had tape over it) and squeeze the putty in so that it was backing its way out of the hole - no air pockets. Putty was thick enough that even at 1-1/2" it did not sag out.
filler mix was wood fibers, silica, and chopped glass
for little holes, especially flat one on deck, those pre-mix glue tubes are very handy.