Well I guess this is related to the fact that if I make a user the administrator of the site, its home directory becomes the root of the site. That's what the Maildir symlink into the user folder is there for I think, so the admin's mailbox will work. To make it all correct, once spamassassin has been activated for the (admin) user, one should also update the .spamassassin folder location correctly, or use a symlink like for the Maildir into the user/ folder...
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