Its my understanding that when using the pit design calculations, to more easily achieve a draft thru the smoker that the height of the exhaust can be increased to equal increasing the exhaust diameter. Which is easier, increasing the stack height or cutting a bigger hole.
It seems to be justified in so much as those who have done the mailbox alts with the increased stack and the mailbox conversions don't seem to ever have any problems with their AMPS. Whereas those who go with just putting the AMPS in the smoker box can have troubles sometimes. <shrugs>
I like the mailbox conversion, the discharge extension, I dislike that I lose vent control and the ability to use chips to achieve it.
I use the AMPS in my box without the conversion. Most of the time AMPS works happily, Sometimes I have to use chips. Me, I blame gremlins.