1. A business like mtgox would expect to be moving coins into cold storage. The moment they need to move coins from cold storage into the hot wallet they would take notice and check their accounting. Theft from transaction malleability would show up in any simple summing of the balances and liabilities. They would notice the theft and stop pulling money from cold storage long before cold storage was empty.
2. The tone is too harsh on mtgox to be a report from a client of mtgox. Who produced it? If you hire a consultancy you can be sure they will brand any document produced.
3. Where did the cash liabilities imbalance come from? The "leaked" financial report did not show them spending the fiat reserve so where did the missing 20M go? How could the fiat liability be unclear? Shouldn't fiat liability be the one thing their accountant has a clear picture of? How do you "average across currencies", you cannot "average" exchange rates, the word makes no sense.
The more I look at this the more it feels like a post on bitcointalk.