I’ve worked as a technician (in my much-younger days) on the flat rate schedules and I ALWAYS beat the book and made money on it. Here’s why:
Removing/Reinstalling an FEL is ONE OPERATION that is charged on the final invoice.
R&R the MM is also charged.
The actual engine-swap operation is flat-rated to include all sorts of procedures that an experienced man knows not to do.
When I worked as a Toyota Tech, I was paid 4.5 hours to change a head gasket the factory had under-torqued. The flat-rate included draining fluids, removing intake and exhaust manifolds completely from the vehicle, pulling valve and rocker assys, pulling the head, cleaning the surfaces, then reassembling all that again.
I could do this job in 45 minutes by opening the radiator-drain into a bucket, and only loosening the manifold studs and sticking a long pry-bar between it and engine to keep them seperated, then leaving the intake/induction system attached to the head as well as the entire valve/rocker assemblies and lifting the head out of the compartment (the antifreeze had drained by that time below the head-level so no fluid is lost.) Scraping the old gskt, installing the new, laying the head back in position, torquing it, bolting the valve assy’s back in situ and adjusting them (I knew to have No 2 cyl at TDC on that engine which has ALL valves closed so no need to rotate each cyl to adjust valves.). Pouring the bucket of antifreeze back into the radiator and bolting the exhaust manifold back onto it’s studs, and it was ready to start.
I would do 4 or 5 a day and make two days pay. Got me all the way thru pilot training and college.
In my experience, I could beat the flat rate manual on all jobs except rear differential gear-set changes (because of an extensive process involving dial indicator/torque-meter bearing pre-load tedium-tasks unique to their early cars.)
True, flat rate manuals could not be beat on old dirty equipment tho’, but it’s a good starting point for guestimates, IMO.