The pad to rotor clearance on hydraulic calipers set themselves once you've bled them and squeezed the master cylinder, that's the beauty of them vs. mech calipers. Clamping a spacer between them when bleeding won't set the clearance that only works on mech calipers. It won't rub, and if it does that means one of the pistons is sticking which you can usually fix with a little penetrating oil and a c clamp.
for mounting, you want to set up and bleed a brake system then clamp the caliper onto the rotor so that the rotor has a few mm of clearance between the bottom of the caliper. when the caliper is in the desired position use that to create your brackets.