The car will be under warranty so unless your keeping it longer than 3 years then I wouldn't worry about the tranny. Then If you do keep it buy and extended warranty. It's that simple.
Something else to consider: my buddy just bought a 2012 stage 3 roush for 40k, even though there is one year left on the warranty he bought an extended one $2500, bought the "phase 3 upgrade" from roush $1500. Puts it at 675hp/585tq flywheel. All while under the warranty since it's from roush even at that power lvl. Tranny blows? That's what your warranty is for. But that's the most that roush offers so if you want more power then you'll have to go a different direction. My buddy spent around 50k after everything and has the same power and warranty as your looking at. Yea it doesn't have the aluminator motor but you have a warranty for that.
Then for that price you can get a 2013 gt500 though which is what my choice would be with the better tranny. Decisions:rolling:
I believe the warranty on the stage 3 upgrade only covers the parts purchased with the stage 3 not any other engine components. You may be able to purchase an aftermarket warranty for a stage 3 but Ford ESP does not cover. Even on a brand new Roush stage 3 you are being covered by a Roush warranty not a Ford warranty. If being covered by a Ford warranty is an important consideration Shelby is the way to go. If not it is just a matter of which car you like the best.
The Roush website also indicates the 625 hp engine is a parts only warranty.
The 2013 Stage 3 Mustang Premier Edition shares the stage 3 power by increase the 5.0L V8 engine with the ROUSH TVS R2300 Supercharger to 565 and 505 ft-lb of torque tire shredding level. Producing all that extra power can make you stress about your Mustang warranty which is no worry due to ROUSH providing a powertrain warranty with a 3 year / 36,000 mile drivetrain warranty. Premier is also available with an optional post title upgrade of 625 horsepower and 525 lb-ft of torque however the powertrain 3 year / 36,000 mile warranty becomes a parts only warranty.