If you own the exchange (or indeed if you 0wn it) you can publish whatever you want in the orderbook if you want. No need to execute the actual trades.
Because it is non-trivial to generate a computer system that creates realistic looking trades in an order book. If you generate fake trades, then pretty soon it will be obvious to everyone that something is very wrong. Generating realistic trade data is something that requires a small team of programmers, who you can't afford because you are in the hole.
Madoff had programmers that did nothing except work on algorithms to generate fake trades. MtGox didn't have the money to do this.
Quote
If you want to steal btc or fiat you just transfer it out. Why trade with yourself first?
Because you are not trying to steal BTC or fiat. You are trying to cover up a theft that was done by someone else.
I don't know about the details of the initial loss of bitcoin, but if you replace the first paragraph with "X loses a lot of bitcoin" then the rest of the story makes sense.