The right click on the axe definitely doesn't work with witchery saplings. I haven't checked other mods... but it would be nice to have a config or something for it to add saplings. I also imagine the same applies with the pickaxe right click and say ticon torches.

It uses a regex pattern to determine what items it can use, if the saplings aren't registered then they have an odd name, I'll ask emoniph.