Try lowering the Yaw P and I a bit to
ATC_RAT_YAW_P,0.8
ATC_RAT_YAW_I,0.08
at least until the rest of the tuning is sorted out and you can verify if values higher than 1.0/0.1 are OK.
Change your Harmonic Notch filter settings as follows:
FFT_MINHZ,30
INS_HNTCH_FREQ,44
INS_HNTCH_BW,22
INS_LOG_BAT_OPT,2
The question you asked about Loiter stability - it’s affected by vibrations and GPS position. This means the aircraft is constantly trying to correct or follow an ever-changing position. You wont see this affect in Stabilise or Alt Hold since they are not relying on X and Y axis position data in the same way as Loiter.
Vibrations are acceptable, not great, but should be good enough. Anything you can do to reduce vibrations further would be worth the effort.
Your GPS1 has a better, more stable update rate than GPS0, but it takes longer to get a good HDOP.
You might want to set FENCE_ENABLE,1 which will force you to wait for a good 3D fix, especially since this is a big expensive and dangerous aircraft.
Experiment with GPS_GNSS_MODE and GPS_GNSS_MODE2 to find what works best in your area. Maybe 5 for GPS and Galileo or 65 for GPS and GLONASS.
In my area there are lots of Beidou sats visible but they give an unsatisfactory HDOP.
Less constellations can mean a faster fix and more stable position data, better update rate.
You might also want to set the best GPS unit as primary GPS_PRIMARY,1 and GPS_AUTO_SWITCH,4 to avoid unnecessarily switching GPS units.
You can see on the map where the IMUs and the GPS units all think they are positioned - ideally these lines would all be much more closely overlaid.
In that pic you can see GPS0 is more closely aligned with the IMU position than GPS2, but that would be because it gained a good 3D fix first and became the primary GPS by default. Experiment with the GPS_GNSS_MODE values (both GPS units would be set the same) and the Primary/Autoswitch settings.
It will be worth doing another Autotune if that all works out OK.
