mcfan2 reports:

Is there a way to make the compost bin actually create vanilla Bonemeal?
Compost looks nicer but it doesn't work with Immersive Engineering's Cloches. Putting minecraft:dye:15 or minecraft:dye@15 doesn't work.

https://minecraft.curseforge.com/projects/composter?comment=5

Still have same problem. Even items without metadata.
minecraft:dye:15 | ore:dyeWhite | minecraft:iron
Composter seems to work, but after process complete nothing shows up in result.
P.S. Sorry for bad eng(

You need to use "minecraft:dye@15" to get bonemeal.

In the next version, I added a "bonemeal" shortcut for you.

Here are screenshots of it working: