Can't tell if this comic just doesn't get it or put zero thought into it. And there is several examples throughout the various series where two ships don't align to each other.

There are several reasons why the ships would always face each other, from common courtesy to defensive posturing.

When two ships face each other its like an nonverbal way of saying "we see you" or "you have our attention". Orientation also plays apart in this. Of course there is no real reason to orient so both ships face "up" thanks to artificial gravity, but it's also something that could be seen as polite and etiquette as getting on the same level as the other meeting them half way.

For defensive purposes, it also makes sense to nose towards a potential threat or adversary as within star trek the shields are strongest at the front (thanks to deflectors and navigational shielding) as well as the best/most accurate sensors to get a good reading. Additionally the forward arc of the ship will likely have the most overlapping weapon arcs, especially for ships like klingon bird of preys with fixed disruptor cannons facing forwards. This posture also tends to keep primary engineering, where the reactor/warp core is situated, obscured and defended, so if the ship wants to make a swift retreat their primary means of doing so is less likely to be damaged or disabled, and if you engage an FTL retreat towards a foes rear that foe needs to turn about and reorient themsevles to give chase, giving more time for the retreating party to take evasive action and avoid further intercepts.