I think I remember reading part of it was to reflect Siddig's then current appearance. I think they liked the idea of giving Bashir a beard too. In Control he looked a lot older (considering the time frame was only a few years later) but I think the idea was to project the great deal of stress he was under by that point.
But I do like that the novels for the last decade or so have tried to be more accurate with their covers, including adding a bit of age to the characters from the last time we saw them.
Back in the 80's and 90's the novel covers were often inaccurate. In The Better Man there's a note telling you when it takes place. But a lot of the novels back then didn't have that, and you couldn't go by the cover so a lot of times you were left trying to guess whether it was during the tv series or the movie time frame. The narrative sometimes clued you in, but not always.
About the only way in some of the older TOS novels i could place it, was by what rank Chekov is in the book. He was an ensign through all 3 seasons of the TV series.