Magura rotors are 2.0mm thick, Shimano rotors are 1.8mm.
Magura doesn't recommend to go any thinner than 1.8mm.
Thinner rotors mean calipers have to extend pads further, loosing in turn modulation and getting you a feel of "worn out" brakes. While Shimano rotors are brand new, the brakes will kind of work, but as you'll be wearing rotors out, you'll kill calipers much quicker.
If you've spent that much money on brakes, I would do a normal setup with recommended rotors.
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