Don’t align them by slackening the bolts and pulling the brakes. Align them, with pads pushed fully retracted, so that the rotor is central in the calliper – view with a torch behind to check. Then slowly torque up the bolts, checking that rotor remains on centreline of calliper.
This ^^^
Don’t use the ‘slacken off then pull the brakes trick’. Also you a light source behind to check as above.