I'm not sure if this is allowed as it's "technically" third-party software, but it's a safe, harmless way to make windowed mode work. If you download a program called AutoHotkey (http://www.autohotkey.com/) you can force the game into borderless fullscreen windowed mode. Dual monitor users (like myself) pretty much have to look to a solution such as this.

It doesn't hook or anything so it doesn't modify the game whatsoever, it's purely a windows macro program, if you google ffxiv autohotkey you can find the script to run to make your window borderless and fullscreen, and it works with other games and programs as well, it's really nice even outside of ffxiv.

Hopefully SE does fix this at some point but for now I think the autohotkey solution works really well.