
Basically, scribe the tenon shoulder over the moulding, as others have said.
Top Left shows the kind of joint produced with the scribe and mould cutters, as Jason linked to, which creates a stub tenon which fits into the panel groove. This relies on the glue holding the joint together, great for cupboard doors, no use for house doors. (This was done using Spindle Moulder Cutter Blocks).
Top Right shows through scribed joints, the Sapele one was done on the Tenoning Machine in the background, the Softwood one by Bandsaw/Hand Tools.
Bottom Left, the kind of gouges required to create scribes by hand, are the in-cannel type, i.e. inside bevel.
Bottom Right, when scribing wide rails on Doors etc, if doing it by hand you only need to scribe ½ inch to 1 inch say, the remaining shoulder can be left square, and a section of moulding chiseled away on the stile, similar to the drawing, which is of a frame.
Mark.