A quine-like program could just as well put its real payload in a string with a cryptographic signature, verify the signature, and then eval the string with the string as input; thus emulating the "passed its own sourcecode" format.

Altering the internal structure of an opponent program would be very difficult, but that's not the only way to mutate a program. You can't tinker with the insides of a black box, but you can wrap a black box.

To be concrete: given an opponent's source code, I could mechanically generate an equivalent program with extremely dissimilar source code (perhaps just a block of text, a decryption routine, and a call to eval) that nevertheless acts exactly like the original program in every way. And since that mechanically-obfuscated program would act exactly like the original program in every way, the obfuscated program would not be able to detect that it had been altered. Do you agree?