If you look at actual Gibson Les Paul guitars that have been cut away to reveal their inner fit, you'll notice that the fit of the neck is not on the bottom of the neck itself, but rather, its sides. The very old Les Paul had a small gap (or maybe no gap by mere luck) under the neck. These were the so called "long tenon" neck guitars. Later, to simplify getting the neck angle right, they switched to a shorter tenon with a curved bottom. Fit the sides, glue it in, set the angle while its still movable and clamp it. All the holding of the joint is on the sides of the neck.
Bolt on neck designs do not have wood on both sides, sometimes no wood on either side (V for example). The grain structure of the wood would be liable to splinter if glued on using the bottom only. Its just a different design. Bolt on necks have served well over the decades. Very well!
