The difference is that she's "perfect" insofar that she was designed specifically to be that way in-universe. If she was just an ordinary person who happened to be faster, stronger and more intelligent because of reasons, then that's one thing, but she was born in a test tube, tailored by an egomaniac, and it's something that actually bothers her.
True, though I did acknowledge that in the post you're quoting. She's still a character designed to be perfect regardless. Which was my point. IMO a big part about being 'Mary Sue' is excelling at everything and being perfect. Miranda is a character who's entire story arc works on the notion that she was created perfect. Perfect body, perfect looks, perfect healing, perfect biotics, perfect intelligence, perfect perfect perfect. She even makes a note to tell you just how perfect she is (just facts). The only flaws she has is one from her dramatic backstory (also trope with Mary Sue characters, coincidentally), emotional issues about her faddah and the fact that she can't have children.
She's ridiculously brilliant, she was the head of the project that resurrected a charred corpse. She has exceptional combat skills. She practically operates and runs the Normandy. Her biotics are on-par with that of an Asari justicar if the suicide mission is to be used as evidence.
IMO between Liara and Miranda it is Miranda who ranks top in terms of competence and excelling at whatever she does. Liara, even without the comparison to Perfect Miranda, is a bit of a bumbling child. One who is constantly being one-up'd or manipulated by Cerberus, of all people. If it was Miranda who took over the Shadowbroker's base (this would have actually fitted with the character too, unlike Liara who is practically a different person at this point) I would bet you my space hamster that she wouldn't had lost the base to Cerberus nor should the Shadowbroker's respect be dwindling.
Again, I'm not saying she is Mary Sue. Like Livi mentioned being loved and liked by everyone is a pretty big part of the trope as well and frankly I don't think anyone other than Jacob and romance-seeking Shepard really liked her. Still between her and Liara it's definitely Miranda, imo, that checks off the most marks on the 'Mary Sue' list. If she was actually loved or even liked by the crew it would be a full on Mary Sue.