Which bolt to use when aligning disc brakes?
Should one adjust the caliper on top of the bracket? Or should one adjust the bracket on the fork?

For Magura parts, you'll adjust the caliper. It's impossible to predict what would be the case for every brake assembly that will ever be manufactured, so your question about the future cannot be answered with certainty. But if you ever see an intermediate bracket like that, engineering concerns dictate a very high probability that you'll always want to adjust the caliper itself, rather than the mounting of the bracket it's secured to.
The part secured by the blue screws is the QM26 adapter used to allow the caliper to work with a 203 mm rotor:

The red screws then secure the caliper to the adapter. It is those screws that you need to loosen before aligning the caliper:

The diagrams above are from the owner's manual. The instructions that go with the second picture read in part:

Installing brake calliper

…
Screw in retaining screws top (M6x35)(11) and bottom (M6x33)(12).
The brake calliper can still be moved slightly but only wobbles slightly
Pull and release the brake lever several times
Pressure point is clearly noticeable and does not change.
Pull and hold brake lever.
Tighten retaining screws alternately and in stages to a tightening torque of max. 6 N-m (53 lbf-in). [A7][A2]


Note particularly the last two points. Disc brakes in general are finicky to get adjusted right (well, even many rim brake designs are too), but it's important to make sure you are holding tension on the brake lever to secure the caliper in line with the rotor, and tightening the screws carefully so as to not disturb this alignment.
Assuming you've already done all these things, then you may have things aligned as best as you're going to. The brake pads ride very close to the rotor, and minute vibrations resonate well through the brake parts and bike frame, so the tiniest irregularities produce noticeable noise. Often once the pads have been worn a bit, things get evened out and the noise abates or disappears completely.