I use biscuit joints in lots of small projects, particularly for joining rails to legs. I usually reference from the bottom of the plate joiner rather than use its fence. When I want to make an offset joint, I cut the slots in the rails first. Then I add a large shim plate to the bottom of the plate joiner, using double-faced tape, and cut the slots in the legs.
The offset between leg and rail is the thickness of the shim—no measuring required. I’ve made a set of five shims of various thicknesses for different offsets, and store them with my machine. –Tom Caspar