Mike Goldman originally wrote the challenge such that it calls for one file and one decompressor. However, when subsequently asked whether there can be multiple files, he agreed; thereby he was arguably duped. He didn't say "okay, but there will be a 256 byte size penalty per additional file", he just plainly agreed. This means that the original formula for adding the size of the solution applies: just the file sizes…
Exactly. IMO the challenge-setter is the one being more unfair here, since his metadata-based reason to reject the solution applies to submissions made under the original rules too. He accepted an amendment without counter-amending to cover that loophole, so if he stands by his word, he has to pay up.
It casts doubt on whether he would pay if somebody won by the original rules with some luck. Maybe he has an implicit allowance, that merely two files can't "encode" a big enough advantage, but again, then it's his fault for not addressing that in the new rules.