The winner appears to be Perl, namely the Mail::Audit module (and whatever other modules it relies on). I had a couple of scripts that did gentle transformations of incoming mails. The transformations were supposed to only ever touch the headers, but I used a Mail::Audit object to write back the entire message including the body. I had complete trust that the body would be bitwise identical to the original, but not so.
This is a very unpleasant surprise, I have thought of Perl and the more popular CPAN modules as the good old workhorse which would always do the job efficiently and reliably - if not always legibly :) I intentionally preferred Perl for this task over some combination of procmail, formail, sed and pcregrep which would have worked. My world is crumbling :( -- Please don't Cc: me privately on mailing lists and Usenet, if you also post the followup to the list or newsgroup. To reply privately _only_ on Usenet and on broken lists which rewrite From, fetch the TXT record for no-use.mooo.com.