Probably an oversight, but Amethyst does not compact in the 2 Tier drawer.

That is because Blocks of amthyst don't transform back into shards. At least in vanilla they don't. They are purely cosmetic. the only things you can put in compacting drawers are things that have a reverse crafting mechanism like Gold Block that split down into Ingots and ingots split into nuggets. Same goes for Iron.
Copper, Coal, Redstone, Lapis, Emerald, Diamond and Bone Blocks. They are the classic 2-Tier compacting blocks. There are only very few blocks in vanilla MC that can be used to store large amounts of materials and be broken down into those again. Amethyst is meant to be farmed in Geodes - hence why you can't mine Budding Amethyst blocks. Prismarine shards and Crystals have to be obtained by looting chests, destroying sea lanterns and killing Guardians/elder guardians. Nether Wart has to be farmed as well, as the wart blocks that generate in crimson forests don't revert back into Nether wart. These blocks and materials add a balance to the game and make the player visit certain places again in order to obtain the materials for their builds. If you could reverse craft Amethyst blocks you'd only ever need to mine down 1 Geode and you'd be swimming in crystals...

If you however have a mod installed, that adds reverse compatibility for amethyst and other block such as quartz and prismarine you may want to share that info with jaquandro.