You have a set rate, for time to change pads and rotors.....Then you have set rates to change brake fluid....Then you have the rates to supply and fit the required pads, rotors and/or brake fluid. This is all combined, when quoting up the job....
If there is a caliper issue, ie leaking piston seal, then you would talk to the customer and quote accordingly to repair the faulty parts.
Handbrake adjustment...This is another area, that doesn't need doing with every rear brake pad change, on a commodore.....I haven't adjusted my handbrake in 10 years...Only replaced the rear brake pads 6 months ago....Handbrake lever....3 clicks and the car holds on a hill, out of gear with it on.
The majority of things you have mentioned add extra time, yes....But honestly, how often do caliper piston seals let go? Brake fluid flush.....10 minutes to do? Being generous with that, because that's how long it took me to do mine recently, when I changed master cylinders....Handbrake adjustment....How often? Be a little realistic when replying