I'm not sure what the Sport designation means. In the Madone line, there's the Pro and regular. You got the regular 5.2. It has 30 mm larger head tube than the Pro. So combine that with a 15 degree rise on the stem, the LBS set you up with a higher bar position. If it feels right, you're set.
You have to have trust in your LBS. If you don't feel comfortable after a few miles, go back and have them make some more adjustments. You can get a much higher bar position with a different stem.
By the way, a 100 mm stem with a 15 degree rise is right in the middle of the range. Don't worry about it affecting the handling.