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Um, hello? Bird Portals? Even if it is magic, they are still making wormholes (Rescue Portal FMV, MO) or transmuting the characters into birds (Good endings, AO and AE, AE bad ending).
And the invisibility powers are either bending light rays or turning the characters transparent. That is also breaking the rules of physics.
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Not breaking, just using in ways we don't know about. Curving space will give distortions which can account for invisibility and wormholes are not forbidden by anything