Mogstation money goes to SE. SE invests that money in all the things they do. FFXIV is one of the things that they do. Therefore, some of the Mogstation money gets put back into the game - but don't expect it all to go there, or even most of it.

Mogstation purchases should only be thought of as "supporting FFXIV" in the vaguest of sense. Those purchases support SE, and SE is the company that runs FFXIV. They want FFXIV to be successful, and to continue to be successful for many years to come. So some of their resources are going to be channeled into the game. But SE also wants to create NEW games, so some of their resources will be channeled into those, as well.

SE has not promised that all Mogstation profits will be directly used on FFXIV, and they are under no obligation to make any such promise (in fact, it would be very foolish of them to make such a promise).