That's because I suspect the mechanism dovecot uses is borked and in fact responsible for all those (alleged) time diffs.
As said: this even happens on a perfectly synced host that has very little time deviation according to ntp - but dovecot claims it is constantly off (at *every single mail* that is delivered) by several orders of magnitude more than ntp is stating/adjusting.
Agreed, though I don't see it "at every single mail". I looked at the commits you posted, and at the code around them, but could not find anything obvious.
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