Jeff,
There are two minor reasons not to seat bullets so that the base protrudes below the neck:
1) Often a "doughnut" of brass will form right where the neck meets the shoulder. This can interfere with accuracy slightly, one reason target shooters prefer those short-bodied, relatively long-neck cases.
2) The problem I mentioned earlier, where the ogive of the bullet ends up inside the neck.
Other than that, there's no reason not to seat bullets below the neck, including the so-called "problem" with powder space. A bullet's base takes up the same amount of powder space whether it's inside a long neck or the case body.
The .284 is a perfect example. The neck is short so almost any 140-grain bullet protrudes below the neck, yet the case still holds more powder than the 7x57 because there's plenty of room AROUND the base of the bullet for powder. We could shorten the case body and lengthen the neck, but then the case would lose a lot more powder room.
As a matter of fact, bullets protruding below the case neck are far more common than not. A 200-grain Nosler Accubond, for instance, protrudes just about as far below the neck of a .300 Weatherby case as it does below the neck of a .300 WSM case.
Sure, a .260 could be built on a long action. The only problem might be feeding from the magazine, but there wouldn't be any major advantage--aside, maybe, from being able to use the super-long target 140's. without part of the ogive being inside
the neck.
It wouldn't gain much velocity, however, because velocity only increases at 1/4 the rate of powder space, and 6.5mm bullet is pretty skinny. You can add a little powder room by seating the bullet out a little, but the .260's neck is pretty short, so you can't see them out much further before the neck won't hold 'em.
