Hello,
I have figured it out and I’m writing it down here so it will be useful for the others.
As the default, MNE uses “percentile” (not percentage) values to set the threshold [min = 96, mid = 97.5, max = 99.95].
In other words, clim = 'auto' is equivalent to clim=dict(kind="percent", lims = (96, 97.5, 99.95)) in case of positive magnitude and clim=dict(kind="percent", pos_lims = (96, 97.5, 99.95)) in the case of postive-negative magnitude.
Btw, is there a standard in M/EEG community to set the threshold values?