2x2 recipes don't work in the 2x2 crafting grid in the player's inventory as the recipes have specifically been made for a 3x3 grid, which means you also can't craft them in other parts of a 3x3 grid.

Maybe its coded as shaped and not shapeless recipes?

It surely isn't shapeless because only that shape works.

Definitely not shapeless. This mod uses unslideable and unflippable recipes (which are normally almost never used), to allow more combinations and permutations from a few hard-used essence types.