Recessed turnout controls avoid the problems of people inadvertantly causing the turnout to change direction by accidentaly snagging the control lever. Here is a method that has worked out well on my own personal layout, and has been adopted by several layout owners around the country.
The slide switch controls a slow motion switch motor that is designed to have power applied to it at all times. For solenoid type switch motors that only require momentary electrical connection, use push buttons on the fascia instead.
It is still possible to recess pushbuttons. Simply remove an adequate sized round hole, much like in the above photos, and install a flat mounting plate behind the fascia. The mounting plate can be made of the same material as the fascia. Gluing it in place is sufficient. Then drill a clearance hole in the mounting place for the pushbutton and install it. By gluing several layers of mounting plate material behind the hole location before cutting out the hole, and then attaching the final mounting plate for the pushbutton, it can be recessed as far as necessary to avoid it protruding beyond the surface of the fascia.