I think you got it wrong. It's the feeling about being billed fairly, not exactly the money amount.
For example, a shop needs to charge $200/hour to make desired profit, on the repair bill,
Shop A: labor is billed $200/hour, parts cost $100, billed customer 15% markup. Total $315
Shop B: labor is billed $100/hour, parts cost $100, billed customer 215% markup. Total $315
Shop B will make people feel been ripped off on parts. Exorbitant parts markups do make the shop look shady, not trust worthy. Perceived honesty matters.
A big problem with shops "needing" that markup, is improper billing of labor.
For instance, when I started at my current shop, labor rate was $90/hour, both alignment and diag time were also "package priced" at $90. Okay, whatever. Well now it's $140/hour, and guess what hasn't changed? Either of those jobs, still 90 bucks.
Diag now gets you 35min or so, rather than 60.
My first car today was a 2000 land cruiser, BRAKE ABS TRAC VSA lamps all on. Circuit code for an ABS solenoid. Solenoid is good on the ABS booster/master super assembly, uhh oh, wiring or module issue. Get to the module, find corrosion on a pin. Remove harness connectors, voltage drop between ABS block and module with 1/4 amp bulb, good at 25mv. Drag test pins and clean harness. Remove ABS module, clean with deoxit and diamond files. Reinstall, zero point calibration performed, fixed.
I charged "diag", $90, plus 0.5 for cleaning, removal, install of the module, that's $70. So $160 to find and fix a corroded pin on a module. Brake pad installation labor is $140. This is inherently flawed.
Had another car, EVAP leak. Where have you heard of a shop where pulling seats/panels/wheel liners for access gets you paid a dime? This is more unbilled time, which makes the labor $$$ equation worse, so markup on parts needs to rise to compensate. How many shops who are "by the book" flat rate actually charging the 0.2 per rotor to remove and clean the hub, or deactivate the electronic parking brake? Plenty will write up pads/rotors with electronic parking brake at 1.0, when it's actually 1.6 by the labor book. IMO the issue is often not on the $/hour of the labor rate, its giving things like test drives, pressure tests, partial tear down, etc away or at a reduced rate.