I have the previous generation Madone, the Madone 9 with 700 series carbon. It's an extremely capable bike, the best I've ever ridden. I love it in crits, and see a lot of others here racing it the same way. It does anything you'd want from a road bike. I can't compare it directly to the Cannondale.

The SLR has a little more relaxed geometry than mine, the H1, and a little more aggressive geometry than the M9 H2s. I had an H2 for a while. I had no complaints about how that bike handled or reacted, I just wasn't used to the position. It wasn't uncomfortable, it just felt a little more like cyclocross. To my mind, the question of geometry and how it fits you is going to be a bigger deal when trying to decide between the SLR and the Cannondale.

I'm sorry I can't be more help answering your question about stiffness. To me, bikes move when I turn the pedals. I have a 2006 Madone that I still ride. The position is exactly the same as the 2017 Madone 9. The frame is less stiff against power, less aero and less compliant in the way that makes it comfortable. But it's still a great ride. It surprises me that both bikes basically disappear.

Anyway, I am sure you can be completely happy with the SLR if it fits you right and you like how it looks. If some lab measured 0.2 mm more deflection under some load, and that turns out to keep you up at night, there are worse things to have occupy your mind.