KOS-MOS only beats any superpowered beings in the alternate future where she was in her original form. So it's not canon really.
Voyager himself had the ability to warp space toa degree. It makes note of this in the EP3 Database where you look up his E.S. and it says that its shields are enhanced by his ability to warp space-time.
Only beats any super powered being in the possible future? And what is Voyager, a silly ***** that runs around screaming the roof is on fire; or T-elos whose energy output was 4.75 times greater than KOS-MOS' Ver. 3? KOS-MOS in Ver. 4 is even greater than T-elos--who was constructed by Kevin, the creator of KOS-MOS, who did not get killed in the process of creating T-elos.
I watched and read a lot and I have come to the conclusion that although KOS-MOS did not blast the universe out of existence in the main storyline she was still capable of doing it. Hence why Nephilim wanted Shion & co. to prevent that possible future from becoming a reality. The theory is strengthened when KOS-MOS gets the Tertiary Weapon system implemented to her in her version 2 body.
Damned edit running out of time:
Which IMHO would imply that version of KOS-MOS is even greater than the form as she was meant to be. Then again it all depends on what they mean by "meant to be." Since when the scientists encountered Shion they commented the Tertiary Weapon system was meant to be a part of KOS-MOS and because of the accident and everything that went wrong they could not add it. So after finding KOS-MOS they finally install it on her and upgrade her in the process.