One caliber depth minimum has been a rule of thumb for God knows how long (as stated above). It helps maintain concentricity and reduce run out if the bullet has enough support on the bearing surface by the case neck.
The other rule of thumb is to never seat a bullet deeper than the shoulder (or into the powder column as it were). It can cause weird ignition as well as inconsistent pressure signs (aka "slugging the bore", which I believe is a phrase Mann or Pope coined back in the late 1800's/early 1900's). The theory ran that some compacted powder in the case could be wedged against the bullet as it began to move, and essentially increasing the weight of the object being accelerated, dramatically raising pressures. Since the amount of powder being pushed was variable, the observed results were erratic pressure signs with identical powder charges (some were fine, others were popping primers with the same powder charge). It's also why deeply cupped bullet bases are avoided (or at least that was what I was told by one Chief Engineer, when were talking about this very subject).
Another thing is that bullets can creep, when loaded into the powder column. Resulting in cases with bullets at slightly different depths after sitting over night. The powder basically pushes against the base of the bullet, and based on neck tension, will push them out ever so much. If annealing is not exact, then some will move more than others.
Okay, enough rambling on my part...