Hmm...
To me, the idea of the Guardians being housed in the pillars and beneath Hyrule Castle (the chamber where you fight C. Ganon) was both so that the Guardians could fan out from Hyrule Castle to protect it from attack, and be in place should an attack originate from the castle itself.
So it makes sense to me that the pillars would house them and that the castle would house some of its own (in the chamber).
Also, for me, the fact that the pillars appear corrupted when they rise (instead of being corrupted after they rise) makes sense if you consider C. Ganon's return as more of a volcanic erruption.
When C. Ganon returns the ground shakes, as if he has exploded from beneath Hyrule itself. If he was surging underground before he made his presence known then he could have corrupted the pillars then.
Thus when he shows himself, the pillars do what they were intended to do and activate (by jutting out of the ground), but with them already being corrupted they work in reverse- unleashing the Guardians upon Hyrule instead of C. Ganon.
If the Guardians were underground and within the pillars then this would be why the ones above ground weren't corrupted until they were hit with Ganon's malice after he errupts from beneath Hyrule Castle.
It is also said that the cavern beneath Hyrule Castle and the Divine Beasts house other Sheikah weapons other than Guardians. If Ganon has spent time corrupting said Guardians and weaponry underground then this would explain why he himself and his Blight counterparts are made up of Sheikah technology and weaponry.
I also kind of want to say that the lack of an obvious exit and entrance to and from the pillars for the Guardians is a design oversight BotW is really bad for;
-The Bridge of Hylia clearly has narrow slots for archers to fire their bows at invaders yet there are no doors or entrance points for soldiers to enter anywhere on the bridge.
-Akkala Citadel is clearly a strategically placed fort to combat against invaders approaching from the sea, it has long range cannons and is high enough for good vantage points of the surrounding terrain and oceanic distance. It can also house many soldiers given its size and could easily be used as a stronghold or place of refuge for citizens... but how do you get in?
Why does such an important and interesting place not have an interior in such a massive game?
-The Great Plateau, again, is similar; it's pretty high up, clearly fortified with the walls surrounding it and as the 'birthplace of Hyrule' one would expect it to be so... but how do you get up there? How do you get in? And if you got in where does it lead out?
There is a dungeon within it if you take the Shrine of Resurrection down to it but it is only operated by the Sheikah Slate (of which there only appears to be one of) and this dungeon doesn't lead out into Hyrule and in fact seems to be deeper under Hyrule itself rather than just the Plateau...
...so the pillars not having a discernable entrance and exit for the Guardians feels to me more than a developer oversight, and with how fast and loose Aonuma was with the lore in this game I'm more willing to accept it as an oversight than any meaningful concern to the story.
On the subject of lore, Zelda does indeed say that C. Ganon HAS given up on resurrection... in english. However in the original Japanese script Zelda states that he HASN'T given up on resurrection.
I have no idea why such a change was made outside of intensifying the drama at hand, but such an opposing meaning between both, with the Japanese version being the original point of origin, I can't accept any story or theory aspect to tie to this with any credibility.
There is something I'm having trouble unserstanding about your theory and it is probably down to me either missing it (it's 2:30am) or me bwing a dumbass, but say you're right and timeshift energy helps bring C. Ganon back... how?
We know Ganon to reincarnate, it's what he does. He wouldn't need timeshift energy to do that, yes he was beaten by the Guardians and Beasts in the past but how then does he become reliant on timeshift energy to reincarnate?
On the other hand, if 10,000 years ago he was merely sealed by such energy then those 10,000 years would have been him becoming immune to timeshift energy so he could then take control, kind of like how humans can build up a resistance to poison over time.
Yes King Rhoam was messing about with Guardians and Sheikah tech, but like i said, if C. Ganon started underground then the Guardians and Sheikah tech above ground wouldn't have made a difference. The only way that would have worked would be if all the Sheikah tech and Guardians were built into some sort of software/cyberspace network and I don't think that's the case.
In my head I just can't make the leap to the timeshift energy bringing him back.