I'm going to have to disagree. If you'd go through that test, not many of the questions are actually essential for a protagonist. As a writer, I don't really see your point as being that valid. A good, well designed protagonist should not be particularly high.
If we're going to trot out writerly credentials, I'm one too. I write space opera.
There is no consistent definition of a Mary Sue character. Like pornography, they tend to be "I'll know one when I see one" characters. In fan fiction, they're a lot easier to identify because they're original characters who get written into existing groups of characters and proceed to become black holes of plot and character interaction from which no character can escape. They distort existing dynamics around them like a black hole causes gravitational lensing.
In original works, the protagonist is almost always exceptional, otherwise why would they be the protagonist? A protagonist, by definition, is the focus and driving force of the plot and most of the character dynamics. People usually don't want to read about protagonists who are unexceptional and blend into the background,
especially in space opera. Space opera is an escapist genre that demands extraordinariness from its characters, settings, and situations. Mary Sue-dom is undifferentiable from what is expected and demanded of protagonists.