Are you kidding!? This is Emacs! You can tell it exactly how to do everything. Just advise/redefine the relevant functions. ;) The documentation of ox and publish does not cover everything, but when in doubt, just ask Emacs what code it runs when you do the thing you want to modify.

On my site (https://two-wrongs.com/) there is very little left of the original HTML. I'll see tomorrow if I can dig up the Lisp code I wrote for it.