Because the SCT is one of the only tuners that is supported with custom tunes (actually one of only a couple that can even hold custom tunes) and it has the largest tuning support. Other tuners like the H&S stuff, are more expensive and there's only one guy writing tunes for it. SCT will shut off the check engine light when you do an EGR delete too, others will not. SCT tunes the transmission, others do not. The custom tuning will put down more power and do it in a safer manner. Just read around the site, you'll see most are using this and all the threads explaining why.

As for your Ford warranty... it's a tough call. I mean, by deleting the EGR you're reducing the risks of failure, so it might still be worth it.

FWIW, in all my terrible experiences with the dealers and trying to find a good diesel technician (very few and far between), if you ever find yourself in a situation where you need to get stuff done on the truck, listen carefully to these points of interest....

Tell the service manager as little as possible. Play dumb. They're the one's making the call on the warranty work, though they don't actually do the work. Tell the technician as much info as possible. The best way to get this done is to leave a note in the truck describing issues with as much detail as possible. If you are going in for an EGR cooler failure, and it's getting warrantied, you might try leaving the EGR delete on the floor and slip a $50 bill above the visor, or the tech's favorite beer in the bed... works like a charm.