Although I agree that the krogan -- with their tough, scaly skin, well-protected vital organs, and bony headplates -- would have a decisive physical advantage over the large-but-humanoid qunari in the real world, the Mass Effect and Dragon Age universes (like most fictional universes) tend to subvert their own internal logic to tell an entertaining tale.
In the Mass Effect universe, for instance, we've seen, and heard stories about, scrawny humans kicking krogan ass: something which shouldn't be possible.
So if the right human can beat up a krogan, then the right qunari certainly can.
Therefore the winner of any krogan vs. qunari contest depends almost entirely upon the combatants involved.
Iron Bull knocks the stuffing out of Random Krogan Mercenary 14.
Grunt destroys Random Tal-Vashoth 24.
Those're the rules of fiction. 
I would phrase that sentence more along the lines of "depends almost entirely upon the whims of the writer", but yes.
You did hit a nail on the head; these are fictional characters and the outcome of any fight would be determined by the person that was writing it. Their intentions, their biases, the needs of the story as they see them.
If the good people at DC comics wanted to publish an issue where a normal human toddler with no super powers of any kind beat the living hell out of Batman or Superman, they're perfectly capable of doing that, because Batman and Superman don't actually exist; they're ink on a page and completely at the mercy of the person writing and the person drawing their story.
Having said all that, abuse of trope(the worf effect) doesn't exactly make for good writing. The Kai Leng example is a good case study. They hired a writer who knew jack all about the lore of the setting, read a quick summary about the species, and saw that krogan are the "tough guy" race, so he figured, "hey, having Kai Leng beat one of these things is gonna make my space ninja a super badass", when the whole thing just came off as being stupid. There are ways that it could have been done to make it cool and make Kai Leng come off as clever, but it was just a stab to the back of the neck in all defiance of krogan anatomy.
A lot of it is born out of overuse of the David vs Goliath trope which has long since been beaten to death; these days I'm honestly surprised when a big guy wins a fight in media because the only thing writers seem to think big, strong people are good for is getting their asses kicked to prove how strong the smaller, more relateable hero is. I imagine that at least part of it is revenge fantasies against school bullies.