Visual align
I know your exact problem. Essentially the squeeze method only seats the caliper so far, but the problem is that the rotor can flex as you squeeze the brakes. Let go and the caliper is still seated off-center.
I first do a alignment by hand with the cps bolts just slightly loose. I visually look down into the caliper and do the gross alignment by hand. Then once it's close, I squeeze the lever to lock in the alignment and tighten the bolts. Sometimes it takes a couple tries, peering through the caliper from the front and top to see which side the caliper is bias'd to.
The other thing to check is to see if your pistons are retracting and that both pistons are working together. Sometimes a stuck piston will stay retracted and therefore rub.