This is why the bodgers favourite ‘undo the bolts, pull the lever and tighten them up again’ trick is a terrible idea.
The rotor should be centred in the caliper, not between the pads. If this then means that you have one side touching, its because your pistons are not returning correctly and your brake needs some maintenance.
Hope floating rotors in particular (with the very big rivets) are often problematic for clearance. If you have matching caliper and rotor brand it shouldnt be an issue. Poor quality or badly spaced hubs can do the same too, if the hub body is not correctly centred as per the standards.