He actually had a hand in tweaking Decima too! When he signed on with Guerrilla, they basically hadn’t planned on offering the engine for external use. It was something they had simply developed for themselves. Guerrilla gave Kojima the framework, and went “well you helped develop FOX, so help us develop Decima (the new name for the previously unnamed engine) too.”
The engine name is even a reference to Dejima Island, which was a Dutch trading port in Japan; For much of Japan’s history, the Dutch were the only ones allowed to trade with Japan. So the name has some strong symbolic meanings, with Guerrilla being a Dutch company and Kojima being Japanese.