I was wondering, what does an emulsion contain? Would it be okay if I separated a small bit of the acidic layer+the emulsion when defatting at the acid stage? Or would I be losing alot of alkaloids?

Most of the alks are likely still in the water phase but there are sure to be some trapped in the emulsion. Best to break it before you proceed.
You don't need to defat MHRB, BTW.

Check the FAQ for tips on breaking emulsions (though they are meant more in the basic phase, the tips such as salt, vibrations and hot water bath all work the same), and next time forget defatting for mimosa, its a pre-historic practice that isnt needed at all.

You can recrystallize your final product if its not as pure as you want it.

What you are seeing during the defat may not actually be an emulsion. Oils and fats are pulled into the solvent in the form of greasy looking bubbles.