Well, if acetone gets into the base soup, some of the freebase should dissolve in it and not migrate to the nps, so it could affect yield in the end. I guess the ratio of water to acetone would play a role for the extent of the effect.

One tiny counter question:
I did my first FASA from limonene last weekend, and i noticed the fumarate precipitates very slowly. Do you think adding some neutral dry acetone before adding FASA would be a good idea, to have less viscous liquid and faster precipitation?

Do not consider layer separation to be precise just because it looks precise. In reality there is a cloud of solvent A molecules in solvent B, and a cloud of solvent B molecules in solvent A - the closer you are to the separation line, the dirtier each solvent is. You can shrink that cloud by waiting, salting, etc. but it is always there. Read up on "partition coefficient". Washing pulls is meant to remove some of the junk that has migrated into the solvent.