So he wants $200 in rent for you to live at his house. Pay him that, and he can put it to the mortgage if he wants. Then, assuming it's reasonable for you to save another $200, do so in your own savings account.
It does kind of make sense to pay down a mortgage rather than let cash pile up in a savings account while paying interest on the mortgage. His equity in this house is obviously going to be used to pay for the next one.
But if you break up, he can't pay back your share in cash.
A joint bank account doesn't solve the break-up problem. He could withdraw all the money for himself (or you could).
If you don't trust him 100%, you might be able to write up a contract saying that if you two don't buy a house together, he must pay you $1 for each $2 you spent on his mortgage. But the easiest thing is just to keep your money separate.