IE recognizes that Black Ink Blocks from Mystcraft are fluids, and it fills the machine with a gray fluid, but it in incapable of putting the ink into bottles. (They go through the machine, but they come out empty.) I don't know if this is a Mystcraft bug or an IE bug, so I am posting about it in each mod's issue tracker.

Mystcraft issue here: XCompWiz/Mystcraft-Issues#305

Here is a screenshot: https://imgur.com/a/JCJr7MJ

Would need a specific recipe because there is no universal "bottling" recipe/registry.
Should be easily added with crafttweaker.

As for the fluid being grey, no clue on that, IE uses the Fluid's colours, so maybe Mystcraft is doing something odd with it?

Thank you for the clarification. Is there a method to add recipes from Mystcraft itself? Like blusunrize.immersiveengineering.common.util.compat.crafttweaker.BottlingMachine.addRecipe but without the need to go through CraftTweaker?

I mean, yeah, IE has an API for its recipes. They're free to make use of it.

Ah, found it. Thank you for your help.