I'm not a white knight for any game. I just understand how the business side of MMO development and revenue generation and allocation works to a degree. I'm not claiming to be an expert mind you, just that I have some measure of experience with it. In all likelihood, if the cash shop didn't exist, no you wouldn't have seen the Scion outfits added "just because". Not if they required extra work (which means extra cost) to make them useable for all the races. Every game has a budget it must adhere to in order to create its content. After that initial investment to get a game launched, game developers and their investors are looking to recoup their investment AND make a profit above and beyond. That's why those investors made the investment after all. Now there's a cost associated with maintaining those game servers, paying employees, and for future development, and subs are the primary method of recouping the initial investment and sustaining the game overall.
When a content patch is planned, it has a budget just like the initial game or an expansion has. What content gets made for that patch must fall within the budget or it doesn't get made. When SE makes something intended for the shop, that item is outside the budget. To justify the expense of making that item, its put forward as a way to generate additional income for the company. Those in charge analyze and make projections on how likely they are to not only recoup the expense, but also how much of a profit they expect to make for the effort.
You did mention something of note though. You are indeed correct that our "cash shop money" and in fact even some of our monthly sub money, could be (and to be transparent, almost certainly is) "funneled" into other non-ffxiv ventures. That's entirely intended. How do you think a game company generates capital to make other games without relying solely on investors or to encourage investors to jump on board? They use profits from their existing IP's that are currently generating revenue to fund their new projects and/or to show investors they have some "skin in the game" as it were.
The bulk of FFXIV's revenue is most likely folded back into the game for future development, but its virtually guaranteed that some of it goes to fund other projects. A game company cannot rely solely on a single IP to carry it for its entire existence. Why do you think Blizzard is putting out games like Hearthstone and Overwatch and Heroes of the Storm? They know WoW can't last forever and they need to diversify their portfolio to continue as a business.
SE is no different. But at the same time, those other IP's SE may be investing your sub money into could be highly successful and generate addition revenue that could, in turn, be put back into FFXIV allowing for bigger and better expansions and content patches.