I'll look into firmware, should be rather easy to hack into.
Meanwhile, ran script to capture noise on short ppm/range once again, this time with 30minute sample window and LFILTER ON.
Much closer to MM's 3458A, but still away from Dr.Frank (his results not using scripts, nor autozero, also no NPLC1000).
One thing I noted from reading manual that actual NPLC >10 is not increasing integration time, but just doing averaging of NPLC10 samples. There is other way to set speed, using APER command, with maximum integration time as 1 second. Should try that.
Running now without autozero, 5min window. No errors from meter so far.
If anyone with 3458A want to jump in, just get
this EZGPIB script and
EZGPIB itself. It takes 17 hours to complete run on all ranges/NPLCs. It can be quicker if reduce window
const duration=30; // Acquisition time in minutes / cycle
Final internal view on both sides of meter before shields installed: