I am a bit confused, you ask what is the best substrate and state you are using the worst kind at the moment (gravel) then you again add that fine gravel is also good.
Best is none or fine sand. That answer works no matter what size they are.
Pebbles= no
Coarse sand= no
Gravel= no
Fine gravel = no
Anything that fits in their mouth will need to be small enough to travel through the throat, stomach and intestines without damaging them or impacting them. If you think it would be uncomfortable to poop it out of your body with a very much smaller anus/vent then that is what your axolotl feels as well.
Safest bet is no substrate at all. Fine sand if you wanna make the tank pretty.