My reasoning is this:
Any character main should be able to use each variation that is advantageous to them. For example, Scorpion mains should be able to switch between Hellfire, Inferno and Ninjitsu when the match up requires it.
So, tier lists are based primarily on the match ups (or at least they should be). Considering each character as a whole character, not broken up into variations, takes this into account and utilises the way the variation system was meant to be implemented.
Hypothetically taking Scorpion again. Let's say he wins a third of his matchups in Hellfire, is even with another third and loses the last third. But the matches he goes even or loses with in Hellfire, he wins in Inferno or Ninjitsu. This would mean that Scorpion wins every match up, making him S+ tier, but wouldn't be reflected if split up into variations.
Yes, this is just hypothetical, but there is no scenario where splitting into variations would be a better way to determine a tier list, unless you wanted to know which variation was best for variation specialists.