Doesn't the dot relate to the gear change?
Don't think so, brake pedal height is adjusted via the rod that connects the pedal to the m/c and NOT by rotating the lever on the spline..
I am suggestion you remove this rod to see if that allows the m/c piston to fully return to its rest position.
Measure the exposed thread length and draw a diagram to recall where you started if you choose to try MaxMidnight's advice.
I think Sean might agree, the dust seal as it 'rolls' helps to retract the piston as pressure in the system is released. Also, the rotors aren't perfectly-smooth, they have high-spots which will push-back the pistons along with the dust seals. It's not a huge amount, if it was, you would feel the pulsating under your foot as you braked. A warped rotor would be very noticeable, and it would cause foot pulsating to a marked degree.
If you can smoothly move the piston in and out of the caliper bore with just finger-pressure, there has to be something in the hose or the linkage causing a failure to retract:
a] in the hose, it would be action like a 1-way valve, in an extreme case. I do not believe that's what you are facing here. A narrowing of the hose diameter due to deterioration, delamination, or accumulated crud could delay the smooth, rapid movement of brake fluid. That could cause a dragging brake, and the resulting heat would worsen things. The '
totally-collapsed internally-hose' would not allow the brake fluid to move back and forth. The wheel would lock-up, and you'd have to open the bleeder valve to release the caliper pressure, to allow the wheel to turn again.
b] in the linkage, I'm thinking the pedal isn't properly set-up for your foot, and you are partially activating your brake when riding. If it's a used bike, take the time to ensure that the pedal is set properly for your size.
You could adjust the brake light switch so that a small movement would illuminate your tail light. Someone behind you would easily-see that you're 'riding the brake.'