Always thought it was a joint venture between Nintendo, GameFreak, and Pokémon Company? Pardon my ignorance, not a Pokémon connoisseur by any stretch lol.
It's a confusing one for sure. It's a join venture between Nintendo, GameFreak and Creatures Inc really with each of those owning a third of the Pokemon Company. I'm not sure anybody outside of there knows how it all works for sure. But at the very least I'd assume the majority of development costs go through GameFreak since they are the ones actually developing the games so at the very least all the staff working there won't be in the Pokemon Company's financials.
The Pokemon Company itself is supposed to be "brand management" which definitely includes merchandising, that's for sure. I'd assume advertising too, which could explain the relatively low profits and occasional losses if all the advertising expenses are paid for by them but most of the revenue flows through Nintendo (as the publisher of the games) instead. Clearly they also get the money from Pokemon Go (or at least whatever part of it doesn't go to Niantic) given the past couple years.
To be honest it's mostly guess work, but surely there's just no way they could be including the main games in here. They're not exactly high budget and easily sell like 15m+ each time, there would have to be a lot more profit than this if they were included.