Because it makes it easier to track revenue streams vs expenses in the book keeping. Yoshi P has outright said that cash shop items have to forecast to make enough money to pay for their own development or they don't get developed and he doesn't make that call. That means the resources used to pay for the creation of those items is paid for by those items. Project management would tie into this since allocation of man hours needed for development of projects would be used to calculate how much staff will be needed to produce the desired products. That is what scheduling is. The additional hours needed to produce the cash shop items would be factored into that when hiring and maintaining staff on the project. The expenses, calculated probably in man hours, would then be allocated to their projects and their respective budgets.
Now that isn't 100% for sure how they would do it but considering what we know of how they greenlight cash shop projects, that is the model that would make sense. Just throwing everything into the FF14 budget expenses would make cost analysis and profit and loss reports for cash shop items very difficult and it would be hard to calculate the profit they provided. That information is essential in business planning and in some cases legally required under accounting standards so accurate reports can be produced for regulators and shareholders.
There is no Bean counter saying that because it would make their job a lot harder. Bean counters like clearly stated expense and revenue paired off so things can be tracked much easier. Particularly when tax comes into the picture. Combined with what we know about their forecasting and green lighting of development of cash shop items we know its outright untrue. You wouldn't be getting any of the non-seasonal items in game without the cash shop because they never would have been developed in the first place.