Most disc brake bikes come with calipers that will never adjust right and stay that way. There are a few reasons for this. Did you ever give caliper screws that final torque for tightness and then they always go sideways? The problem is chiefly caused by O-rings. In a bike factory assembly line individual items of nuts, bolts, washers.. are preassembled as components. The caliper component is held together with an O-ring at the bottom of the stack of washers and spacers on the hex cap screw. When tightened part of it gets caught in the threads and the rest protrudes to one side. The cap screws must be pulled and the O-rings worked off for the bike's brakes to ever work right. I can give more. That is a good place to start. I will invite @m@Robertson to kick this thread off.
I have been called a brake whisperer when it comes to adjusting people's brakes for them, and the secret has always been to NOT tighten the crap out of the caliper into the mount. As you say, the caliper can be aligned just perfectly, and that final torque-down ruins it. I don't have any o rings on my caliper mounts, or any others I have had to fiddle with. Its just that cranking down on that mounting bolt with even moderate torque is enough to make it shift (OR to change the caliper's orientation now that it is pressed hard into the surface of the adapter).
So I eyeball it carefully to get the caliper lined up so it has room on both sides of the pad (assuming hydraulic brakes where both pistons move). Then with the wheel spinning I verrry gently torque one caliper bolt so it is barely snug (only!). Spin the wheel again and see if the caliper has shifted. If it has, the other caliper bolt is not snugged yet. Using thumb and forefinger to move the other side of the caliper just a hair until no more rubbing. If necessary start over, loosen the first side and try again. Once one side is aligned and snug, use thumb and forefinger to hold the caliper (while the wheel is spinning) and barely snug the other caliper bolt.
Now you have a caliper aligned perfectly, but its only snug-tight. Alternate back to the original caliper bolt and only BARELY give it some torque. Move to the other bolt and do the same. Maybe go two rounds of this.
In the end you have a brake caliper that rubs nothing but is held in place by only mild torque. Which is fine. Worst case in a few weeks it will come loose and you repeat the process. I also usually use extra long caliper bolts into the adapter so I get engagement on ALL threads in the adapter. So the caliper can not fall off. And really nothing bad can happen since the caliper will still clamp the rotor just fine even if its freely moving and a bit loose.
Look what I just found on my rear caliper mount,..
The other side looks fine, but I think that I'll just remove all the O-rings?
I'll just cake it up good with Anti-Seize instead to stop any corrosion.
I don't see much of a purpose to those O-rings? They just keep water out of the bolt threads I guess?
It's not like any water is going to get inside the caliper through the caliper bolts.
So I eyeball it carefully to get the caliper lined up so it has room on both sides of the pad (assuming hydraulic brakes where both pistons move). Then with the wheel spinning I verrry gently torque one caliper bolt so it is barely snug (only!).