patio11's comment is about donating vs. paying by a business entity. Something I hadn't considered is that a business (even if it's just a one-person developer who has incorporated) can pay for software tax-free to any org as long as it's an actual business expense, since businesses (at least in the US, and I assume in Japan as well) are taxed on their profits, not on their gross income.
Patrick's issue with donating as a business makes sense: the tax authorities will look at a donation and think it's a part of a tax-avoidance scheme, but if the business pays for a license to software (even the payment is essentially a part of a custom license, and the software is also available for free under the same or similar terms), and has that payment documented, it's fine.
This would be illegal in many countries. The business must behave in its best interests. If software is available for free, yet they choose to pay for it, they aren't acting in their own best interests in the eyes of the law....
https://news.ycombinator.com/item?id=10863939