I’m not sure this is making sense: how can you recover money that was stolen if it was stored aside? Has MtGox ever officially explained the reason the BitCoins were gone?
Insider theft or loss of keys seem to be the most plausible theories, though some people think all the money may simply have been gambled away trying to recover losses incurred earlier.
Some folks over on Reddit, btw, claim to also have found an additional 300,000 BTC still under MtGox's control. This is perhaps support for the "missing keys" theory, or perhaps simply "gross incompetence".
Mt. Gox alleged they were stolen via transaction malleability, so yes, it would seem they are "finding" coins that had been "stolen".
This is analogous to saying:
"Have US Dollar ever officially explained the reason the dollars were gone?" after a bank was robbed.
"BitCoin" could refer to the Bitcoin protocol itself. The technical reasons/blockchain could conceivably explain some things, for example.