I'm honestly not sure what configuration of mods you have that causes this, but when testing with just FCT's Barreling Machines, Intermediate Bulk Containers, and this mod; the IBC filling/emptying recipes do not appear in either factoriopedia or in the crafting menu (neither player nor assembler), and they both process correctly in the FTC barreling machine. I also tested with Pelagos, then tested with the planets in the 2.0 version of All Planets Lite, and still couldn't reproduce any of the issues.
I added recipe.hide_from_player_crafting = true, since it wouldn't change anything for me anyways, but might end up fixing the problem for you.
I likely won't be updating this mod to the 2.1 version of Factorio, until/unless FCT updates their own mods first