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Just keep in mind your English copy of the contract is worth about as much as the paper it was printed on. When it comes down to it, the only contract that matters it the one that is filed in...

My contract was e-mailed and mailed.

Just remember you might not be allowed to change apartments until your second year. They could be locked into a lease which prevents you from moving.

For the record, if you don't like where you are living you may or may not be able to move. Your subsidies might also not transfer in that case either. They also have no responsibility to help you...

I would imagine a rent agreement like that is designed for prefectures/areas where rent is difficult to anticipate and they want to make sure that the playing field is fair among all their ALTs....