I know your post wasn't directed at me, but I thought I'd weigh-in...First off, I originally posted those panels from IC to convey the fact that even Alex Luthor was awestruck by the effect that Prime's punches were having on the whole of reality -- he had absolutely no clue how or why such a thing was possible. All he knew is that reality was being restructured before his eyes.
And as has been mentioned ad nauseam: even though Prime had a fixed location/nexus point to strike, that obviously isn't a feat that any random character can replicate. We know this because Kal-L furiously punched/shattered those same walls "for what seems like hours", and caused no repercussions to reality:
https://ibb.co/0ZDTbtB
https://ibb.co/ZGthQ0P
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1.) In that particular scene, the artistic/authorial intent seemed to be that Prime was punching the mirror-like 'wall' of the Phantom Zone itself, imo. Hence this:
Full scene:
https://ibb.co/K6ySPYx
https://ibb.co/2KtXVXR
https://ibb.co/KGbnB1v
https://ibb.co/Kbjg050
https://ibb.co/P5JtLRv
I understand that the PZ having a defined space and/or bordering walls doesn't make much sense, but different writers often do whatever they want in cases like this(especially those involving Prime.) Now as for how punching out of the PZ could have altered continuity: I have no rational explanation for that. The PZ isn't historically defined as a multiversal nexus point(certainly not in the same way the Limbo realm or DN are)... But as mentioned in the above scene- that's just what Prime does(nonsensical as it may be):
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2.) Indeed. When Prime struck the Superman knockoff(aka. "Saint"😉, his native world/reality was altered as a direct corollary:
https://ibb.co/qd4JzGS
Yet when the mainstream Supermen beat the shit out of Saint, his world/reality was never stated(or implied) to have been altered as a result:
https://ibb.co/YXXyRTG
https://ibb.co/mDqC1Qx
At this point it is abundantly clear that Prime's punches have an innate ability to alter/affect reality in ways no other being(barring high-end reality manipulators) can... When connecting with certain 'targets' that are in some way intrinsically tied-to creation.
This is an 'ability' that even Rip Hunter mentioned(and found ridiculous) after the events of IC:
https://ibb.co/sKxxMfG
"Everything in history predating the re-creation of the multiverse has gone malleable. Thanks mostly to Mr. Mind and that Kryptonian boy's tantrums, which I still find ridiculous to believe...Punching history. Please..."
But it is what it is... /shrug
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3.) Indeed. The battle between Perpetua and DN was being waged across every facet of reality, for multiple issues(to the point where the Source/Overvoid sent in the Chronicler to observe the multiverse's end):
https://ibb.co/bg6MSzx
https://ibb.co/whYLdWV
...Yet even Perpetua's attacks were never implied to have subsequently altered DN's creation in a similar manner to Prime's strikes:
https://ibb.co/LY0LZjj
https://ibb.co/51KvGJW
https://ibb.co/C04WWcv
Not sure why Prime being able to punch continuity so hard that it switches forms is being lowballed/downplayed to such extremes..? The fact that it is completely illogical doesn't change the fact that he's... Done it. 😕