I mean, she did use NIGH OMNIPOTENT ELDRITCH HOOPTY to, in essence, become Fluttershy.  
It’s not too much of a twist to overextend on that goal.

@Background Pony #CE91  
Or, and hear me out here; there are no rules, nothing has an explanation, and just goes the way Grim feels like with no limitations.

@BigOnionbean  
It could be that since spending her time with Discord and undergoing her own Draconequus transformation, Fluttershy has essentially grown beyond the psycholimitations of both her original body to “ascend” to something as great as Discord and Cosmos are. However, whereas Cosmos has only been filled with a singular desire to consume and absorb to become stronger; it is all externally generated. She’s basically only wearing a bunch of coats to make herself look bigger while Fluttershy naturally grew bigger and as such has the capacity to overpower Cosmos due to her innate connections with whatever nigh-insignificant motes is ultimately left of her friends and family as the anchor to undo all that Cosmos has attempted.

🤣👏

I’m reminded of that Evil Meteor from the Grim Adventures of Billy and Mandy who ate Mandy’s brain and wound up losing.

Meh, I still find it ridiculous that Fluttershy would be enough to tip the scale against Cosmos. She is all but one stone in a tide that is Cosmos, one element against the universe….
 
If anything as in a past comment I said, this wouldn’t really be Fluttershy but rather Cosmos wearing her like a skin costume, a proverbial flesh mask of false existence that Cosmos can fool and convince discord that she is. Getting both her desire of being with him, though there could be an irony in her having to conform to the very bane of her jealousy in order to be with him…

well done flutters, I am looking forward to seeing how this plays out.

Oh I get it, because of the…  
Hmmmyes, it all makes sense now.

Seems like I had the right idea: Cosmos did try to bite more than she could chew with Fluttershy.