I believe that some characters are low in the list, simply because, they dont have good reps yet.
Prime examples are Goro, F/T, Jason (especially after the buffs/fixes he received), Liu Kang and probably Mileena.
Mileena especially, might have risky mix ups (and since we are humans we wont be able to block her mix ups all the time), but she can deal good damage with one bar, has above average zoning and good armored anti-wake up normals. Also her hit box is not something to not take account into.
Being a Goro main, i really cant accept that he is last in the list, especially KW variation. That means that he loses against the entire cast, which is not true at all. Yes, he has AA issues, but that alone does not make him bottom 1 lol. There are others who also have AA problems as well, including some of the high tiers.
His worst MU's are KL, Tanya and QC. Other than that, the rest of his MU's are highly winnable.
Same with F/T, especially Vicious variation. You can put a character who is the safest in the game at everything, has excellent range, corner pressure, good AA's, very good meterless damage from both the low and overhead combo starter and excellent anti-zoning tools, at the bottom, if you havent explored him yet.
So, all in all, i believe this list is about the representation some characters have gotten until now and we are starting to see the results of those characters, while others, remain, mostly, unexplored.
Bottom line,
Too soon for a MU chart people.
P.S: I am writing this taking into account what OP said. That even if a character is low tier, it does not mean that he/she is not viable.