Japanese taxation

I am no tax expert. In fact, the class I most suffered through in my college days was Taxes. However, I know a case of tax lunacy when I see it... at least in my humble gaijin view:

The signature of a contract in Japan is taxable. No, it's not a notary's fee. It's a tax that everyone must pay upon signing a contract. No, it's not the value added on the goods or services associated with that contract either (those come later). It's a tax payable exclusively on the signature of a contract in Japan. If there is an amount stipulated on the contract, the tax is proportional to that amount (and rather hefty). And if no amount is stipulated, then there's a nominal fee. All contracts between two parties located in Japan are subject to the tax. What if the contract is between someone in Japan and someone abroad? Then the tax must be paid only if the Japanese party is the second one to sign. Hmmm??? Don't ask, that's the way it is.

What happened to the principle about avoiding double-taxation and all that boring prose I had to study 15 years ago? What is the rationale for paying if you're the last one to sign but not otherwise?

Well, like all things in Japan, taxes here follow their own logic. And my small gaijin brain can't quite comprehend...