I have a Banks exhaust, but I bought my SMB used with it already installed, so I have no comparison. I had the turbo replaced under warranty with no issues. I have not seen any computer issues.
I've seen many warranty horror stories posted on TheDieselStop.com from people how have used programmers to gain more power, and Ford then voids their powertrain warranty. Maybe after my warranty is over I'll consider a minor power increase via a programmer. Chips and tuners leave behind an indicator that Ford can use to check if one's been installed, even after it's been removed.
I do have a Mag HyTec high capacity trans pan as I viewed it a cheap insurance for towing, and for the same reason, I have a BD Power X-monitor to keep track of EGTs, trans temp and boost pressure.
SMB-less as of 02/04/2012. Our savings account is richer, but our adventures are poorer.