Having no step-down from rabbet to filler is the best fit, so we always fill the rabbet. Dustcover paper lays perfectly and there's no chance of finger poke-through.
The Fletcher "MultiPoint" (yellow) driver is the tool of my choice for that happy situation. Just tip the nose of the tool into the rabbet, pull the trigger, and then flatten out the tool on the back of the filler board as you pull the tool away. Each MultiPoint bends to lay flat on the backing board. And if necessary to reopen the frame package to remove previously-unseen debris, the MultiPoints will bend up and back down again a few times.
I often add strips of 2" clear polyester packing tape with non-migrating acrylic adhesive (3M "Super Heavy Duty") all around to cover the fitting points and smooth the assembly under the dustcover paper. That also closes the frame package tighter and gives the frame extra corner-to-corner stability.