I really think it comes down to what you are looking for in a mustang. I have seen many high mileage reviews of the coyote engines, and there do not seem to be any longevity problems with the engines. So it really comes down to what you take preference over.
If all you care about is having the power, then ya, I say pull the trigger. For $40k, your getting a bare bones GT, but on the other side, its a bare bones GT with 727hp. And you are able to finance a $7k blower setup at a low interest rate. As far as long term reliability, I think you'll be ok. The stock blocks obviously weren't designed to push that much power, but they can handle it. If you're going to be going out everyday pedal to the metal, that might be a different story and eventually you will have problems with the drivetrain. But if you're going to be daily driving to work and everywhere else like alot of us do, you barely use 200hp a day as its mostly just highway driving and normal load conditions. In that case, having a blower shouldn't add any more ware and tare on the engine. The occasional WOT and opening the thing up should be ok on the stock engine... should be.
Now, if you are like me, and daily the car to work, grocery store, and everything else, I would prefer to put the $40k into comfort. My 2012 GT is fully loaded and I wouldn't give it up for a blower. As much as it would be fun to rip threw the gears with that much power, I think having Navigation, leather, and all the other gadgets is better from a daily driver stand point. I guess I would look at it different if I was to own two mustangs or performance cars.
So those two things being said, If I was on a budget of $40k, I would go with a premium package and be happy with the 435hp that comes stock. But, If long term goals was to boost the car, and I could manage a little higher payments, I would have them put this package on a premium GT and just have a higher payments.