Unless Ed Boon purposely meant for that to be in the game, Quan Chi wasn't designed with it in mind. Quan Chi just ended up with it because of a player experimenting with him. It's an oversight at best.
It's also not a "thinking man's setup." It's literally touch the opponent and do the string into the rune. Wash, rinse, and repeat. Not much thinking involved there.
The only "precise math" involved was Mayo expanding on it.
All right. It seems to me as though there is a breakdown in communication happening.
So, I will attempt to explain to you what I mean by "Thinking man's set-up."
On the outside, to someone who does not main Quan Chi, it's easy to ONLY see 11 xx Sky Drop, 212 xx EN Rune. However, it just isn't that simple. Meter management and math is absolutely crucial to playing this character. If you don't understand the amount of meter you're building off of blocked hits and special moves, it could spell the end for you. Specifically, knowing your totals and doing the math could mean the difference between a three EN Rune Trap and a Four EN Rune Trap. Also, if you did not do your math properly and you do a 212 xx regular rune, you will get punished, in some cases severely. So simply doing 212 xx rune until the cows come home doesn't cut it. You have to THINK about your meter/math management.
As a Quan Chi main, you need to intuitively understand how many hits you need blocked, how many special moves you need to whiff in order to build the next bar. The precise Math was discovered by Mayo, yes, but all serious Quan Chi mains use it.
Also, there seems to be this argument circulating that The Rune Trap was some kind of flaw or glitch. Let's say, for argument's sake, it was. Quan Chi was never meant to be able to do The Rune Trap. If we are to assume that this is true, then we need to look at the rest of his tools.
Looking at these tools, what kind of character is Quan Chi?
Is he a Rushdown Character without The Rune Trap? Not likely. With an 11 frame d1, 11 frame starter on his fastest, high-hitting string, and a d3 that grants hm very little advantage and no real frame traps outside of EN Rune, it does not seem likely that he is a Rushdown Character without The Rune Trap.
Is he a zoner without The Rune Trap? He has zoning tools, certainly. Regular runes and skulls serve as decent zoning tools, and trance does trade favorably with many projectiles in the game. However, if we compare his zoning tools to actual zoners in MK9, we again see that he falls short. Add to that the fact that he has no real normals with significant range outside of d4 and f1, and we can see that he wasn't meant to zone with normals, either. Also, he only has a slow d1, an average d3, and an uppercut for defense. As a zoner, surely he would have better defensive options.
So, he most likely isn't a zoning character without The Rune Trap.
So...what is he?
If you look at the fact that he builds significant meter during blocked strings and jump-in-punches, and that he can whiff special moves for more meter during trance, we can AT LEAST agree that he is very meter reliant.
What does he use the meter for?
EN Runes. EN Trance. EN Sky Drop.
The EN Sky Drop really should only be used for defense, EN Trance only drains a bar and can't really win you a game by itself. So the onus falls to EN Rune to pick up the slack. Now, given EN Rune's special properties and how the character is designed to be meter dependent, are we sure we can make a case that his design was some kind of accident?
I'm sure you do, as much of what I'm saying is speculative, but I think what little evidence we have leads itself more toward The Rune Trap being intentional rather than not.
Of course, there is no hard evidence to firmly argue either way, so it's speculative at best.