It does seem better to go "this takes place before the current eps" but I guess the fear - and likely correct! - was fans would turn their noses up at such a book for not 'counting'
I'll have to check, but amazingly, I don't think that was brought up in that comic.
Since writing this, I have read the Emissary novelisation, and a lot of the deleted scenes do involve Keiko (I think her narrative was shifted into the following episodes). There's also a lot with O'Brien, including him flashing back to the incidents in the Cardassian War mentioned in "The Wounded".