Alternate theory #2,
The increased surface area of a low case fill charge causes more powder to burn at once, increasing pressure faster than one would expect for a slow powder, until detonation heat/pressure is achieved. Filling a 300 Win Mag case to 50% fill would expose a lot more powder to the initial flame than a 90% case fill. If the primer flame ignited all the powder at the top of the stack causing the powder to burn downward this makes a lot of sense.
Normally the primer flame is contained towards the rear of the case by packed powder, and the powder burns from back to front (unless you modify your cases for frontal ignition).
Anyways, the SEE is real and there are lot of ways it could happen, at least in terms of physics/chemistry.
The problem with being a scientist is figuring out exactly what is happening. The problem with being an engineer is figuring out how to keep it from happening.