It's worst than that, for remember the main Mt Gox was just one of many exchanges owned by Mark Karpeles. There were several in different countries using different banks.
I'm just wondering how Mt.Gox (and other brokerage sites) actually work? Do they have actual branches of their banks or is it like a separate company that holds a bank account and sets up a database of users to transfer funds to separately? I know Mt Gox's bank is in Japan but is the company also hosted there. Just very confused with regard to security and how they're set up to make all this happen without any pressure from banks or governments. So how does something like Mt Gox actually get set up? Still researching a ton about BTC in general and have a lot of questions but this one was kind of nagging me.
Actually, MtGox is more than just Japan.
Our head office is located in Tokyo (in Shibuya), and we have branches all around the world. For example for European deposits, we have a bank account in Poland held by MtGox Poland.
We comply as much as possible with local regulations in countries where we are present, and always look for opportunities to make our activity more compliant. In Japan we discussed with the FSA ( http://www.fsa.go.jp/ ) and were told that our activity is fine as it is now. We are also working with authorities in Europe and US to ensure our activity is in line with local regulations.