Lot of differing opinions here
My experience has been as follows
Always reprogram my vehicles as soon as the the software becomes available
Have had my 2013 Taurus SHO on the dyno rolls for state inspection (In Arizona) twice with Livernois 93 octane software installed & passed ok.
Have taken it to the dealer for SYNC issues & left the calibration installed & no problems
Traded my 2011 F150 in with 93 octane tow calibration left in PCM & told dealer & no problems
Traded my 2013 Flex with 3.5L eco boost & Livernois 93 octane perf/tow software still installed & told dealer & no problems
Traded my 2016 Explorer sport in with Livernois 93 octane perf/tow still installed & told dealer & no problems
2 different dealers & no issues
Do not know if they reflash the PCM to stock or leave it as is so they perform much better than stock
If I could not reprogram the ECO Boost vehicles I would not buy them
They have so much untapped potential It is a shame the Ford calibrators do such a poor job with their software calibrations
While I often see comments regarding the electronics on these vehicles I do not fear them
From my perspective the electronics make it much easier to calibrate the vehicle the way you want it to run & make it much easier to diagnose problems if & when they do occur
When you consider the current common rail diesel engines, they come calibrated for over 1000lb ft of torque from the factory now
You can easily reflash the PCM on them for 1200-1300lb ft of torque along with the trans reprogramming as well & they perform very well.
No need to replace any mechanical components to do so
Retired fuel & emissions engineer (73 years old now).
Worked for over 40 years developing Oxygen psensors & other engine sensors & controls
Worked with the powertrain engineers at Ford, GM, Bosch & NGK
Probably why my perspective is different than many folks who have not had that experience
I respect your time in the engineering side for oem applications, and you've been fortunate with you selling your tuned cars. Most dealers will often just send those to auction and not say anything about it. The major electronics issue has nothing to do with the electronics controlling engine operation, it's the fact these cars are all fly by wire and everything from power distribution modules, selonoids, relays, servos, and basic switches are all prone to failure more so than mechanical components. Fly by wire tuning is great though and as you know many engines are tuned down to leave wiggle room for future model power increases using the same platform.
Back to the diesel stuff though, the dealer advertised numbers are greatly over inflated and I've seen a ton of heart breaks when someone thinks their truck is xxxhp/xxxxtq.
Take this 2017 powerstroke for example.... has upgraded turbo, dual fuel pumps, ppei tuning which is a reliable tuner, high flow intercooler and piping, all of which are easily over 7k+ in bolt ons not including labor and tuning.
It makes a sad 620hp/10xxtq at the rear wheel, which near that same power with around 600hp/1100tq can be had with just a deleted and tuned Cummins or Duramax.
I specialize in un-engineering and improving oem applications to the way they should've come from the factory.
Factory!
My personal Cummins 6.7 makes around 1400hp/2300ftlbs at the rear... runs 64.5sxe/etr488 v2 Borg compounds and has enough fuel to keep and Eskimo village warm through a blizard....