After posting this message I went outside for a cigar and immediately realized several things. First the file/folder thing cannot be hacked.
Second, the TPM bypass in the GreenWave article will be fixed by Apple in the next developer's agreement. It will say that anyone playing the game in the story will lose their license, may be terminated as a partner and may be prosecuted. The developer kit situation is a special case by which the source code must be released. It is the only such case.
In a normal consumer situation, backup CD's come with the system and they are, I think, only in binary. Further, if Apple buys the MAcTel MB's from Intel (or whomever) the TPM will have the Endorsement Key burned in. Apple will have all the Wave server software like ACM and KTS-AD. The consumer unit could and should have the backup CD's encrypted against the TPM for that Mac, ensuring only the MacTel can run the software or receive updates. This is what SKS should have said in his reply.
Sorry for not thinking the issue through before. Ready! Fire! Aim!