Yeah, buying directly is a bit convoluted.
I'm not interested in buying this game right now (since it's incomplete and the author isn't really inspiring confidence that he'll complete it based on his blogposts) but last time I tried It's easier to just buy DMM points using paypal or credit card then using the DMM points to buy the game.
You must be registered to see the links
1 DMM point == 1 JPY so you can just buy the exact amount of DMM points. After you choose a payment method scroll down to the bottom and there is an input box there that allows you to type the exact amount of points you want to buy.
That's what I did when I bought a game from DMM before and it works fine.