The thickness of the hats on the flange is nominally 1/4". (about 6.35mm) That shouldn't adversely effect the tire to fender clearances.
The hats are available in different offsets so you should basically be able to find a combination where you do not need to relocate the calipers.
Part of the thinking with separate hats/rotors is that it becomes somewhat of a modular system giving you much more flexibility of the bake system.
You MAY need to shim them to center the rotor on the caliper though? In fact that is very likely. Hardened shims are available from hardware suppliers. Those are very similar to the thickness varieties you would use for shimming valve springs with selections from a few thousands up to about 1/8" thick.
None of this is rocket science.
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