I have a 7.3 PSD with a Banks system and had no problems with Ford warranty coverage. Banks I know specifically state they do not exceed engine tolerances with any of their stuff, and you have the ability to remove or bypass any electronic components for testing purposes. Banks has a limited lifetime warranty on their components (5 years on electronics I think) and has worked with folks in the past to get around imagined warranty problems with their dealers. The only catch is you have to prove it's not the add-on causing the issue before Ford will look at it, so be prepared to spend a bit of time explaning and testing for them.
One nasty caviat - if you leave the Banks chip in, the onboard diags will report a memory error to the diagnostic console. Make SURE you remove the chip (it's under the dash and fairly accessible) before you have any serious diagnostic work done. Otherwise they'll replace the computer and your chip may go with it.
On a side note, I've not had any engine related difficulty with the Banks in my 7.3 PSD, and I'm up to 108,000 miles, and had the extended warranty from Ford on the vehicle. I had a few items replaced under warranty, but nothing really engine-related (I did smoke a tranny in S. Dakota, but McKee Ford in Rapid City gave me no trouble over it).
It's a risk you have to take if you go that route, but the major units have been around for a while and so long as you go with something reputable, you should be able to get support and assistance.