"The underlying mathematics behind why six confirmations is a fairly safe threshold is independent of block confirmation time, so the Primecoin transaction at six confirmations is no less secure"
I think this is wrong. 6 conformations in Bitcoin means that 1 hours worth of work has gone into sealing the transaction into the blockchain. To invalidate these 6 blocks you would need, for example, twice the compute power of the honest nodes for 2 hours. With primecoin you would only require this power for 12 minutes, which is 10 times less work.
Lowering the confirmation time only increases the granularity of the confidence in a certain transaction over time.
I think this is wrong. 6 conformations in Bitcoin means that 1 hours worth of work has gone into sealing the transaction into the blockchain. To invalidate these 6 blocks you would need, for example, twice the compute power of the honest nodes for 2 hours. With primecoin you would only require this power for 12 minutes, which is 10 times less work.
Lowering the confirmation time only increases the granularity of the confidence in a certain transaction over time.