I run through the tuning and it removes the PID settings from the "standard" entries and puts them at the end of the printer.cfg.
I run the configurator to change the nozzle size and it puts back the PID settings the tuning removed!
AND it removes any custom entries I had!!!
RatOS v2.1.0
Base image: RatOS v2.1.0 (bullseye)
Updated to: v2.1.0-0-g0be29e9d