All of the latest information has pointed directly towards dry conditions. Remember that tortoises that don't come from humid areas spend a great amount of time in very humid burrows. Most tortoises you see with pyramiding were kept in nearly bone-dry conditions.
Extra protein makes a tortoise grow faster, which can make pyramiding occur more rapidly, but is certainly not the cause of it. Lack of calcium actually causes the opposite of pyramiding. It causes the shell to sink in as it becomes softer. The only reason it is so often associated with pyramiding is because tortoises kept in poor conditions will typically acquire both traits.
If anyone has the february 2007 edition of reptiles magazine, it actually explains the process of pyramiding and why it is caused by dry conditions. Unfortunately, I cannot find my copy of that particular issue.