Well SWIM never understood how could people use a separatory funnel (or in this case a carboy with spigot) in an stb. The lower acqueous part sticks to the walls and everything. Remember the acqueous thick liquid is what will be drained out and the naphtha with some remains of black liquid on the wall will be on top (so more possibility of contamination). In an A/B. sounds more doable as one only deals with a filtered liquid.
Maybe finding another way to separate the layers. Like using a tube to suck off the top layer more crudely (you know like getting gasoline from a tank, using an initial vacuum and the gravity) and into a taller thinner container. No problem if some of the black basic liquid comes together, because in the thinner taller container one can decant most of the clean naphtha and then accurately pipette the final bit away.
Just gotta thing of a propper way to make the first vacuum force. SWIM once tried with a vacuum cleaner straight connected to the tube, but it just sucked stuff way too fast through the tube (and into the vacuum cleaner). But what one could do is make the same principle as in a vacuum filtering system, so that the filtered liquid doesnt go to the vacuum source (like using an hdpe container with a tube from the top where the desire things will come, that goes down to almost the bottom, and another tube coming out of some top side, where the vacuum source will be. So the vacuum liquid fills the bottom of the jug and due to gravity dont jump to the top part where the vacuum source is). And then from this container used for vacuum, just pour into a thinner taller container and proceed as mentioned before
its an idea at least, I guess there are other possibilities one can think of