It's not "just a couple of hours" (I know exaggerating) they actually talked about it in one of their last livestreams, they have to update FFXI beyond DX8 to get it to properly work, the framework is just too outdated and SE isn't allocating much funds to XI with XIV's new expansion being their focus of the MMO division.
**** only reason I use Windower was back in the day for the performance of the windowed mode vs XI's windowed mode, but these days if they're able to update it to DX9 or 10 like they planned to things will be a lot more "modern", since they said the sole reason the new UI they were working on is in limbo is because of dev costs associated with framework upgrading. So we probably won't see much until after March at minimum (financial period end etc.)
As for commands, it exists - It's even more of a botting program now lol, so some people literally can't live without Windower now because of all the features of W4.
Uh.... I think they're full of it as far as Borderless Window goes.
Windower is nothing more than an API hook that forces PlayOnline to allow Windowed Mode in a Borderless Window Mode. It's a hook that injects code into the .exe. The same code that SE could just put in the .exe themselves. Windower isn't some piece of magic that suddenly makes a DX8 game run like it's DX9 or something.
If a third-party developer can do it with an API hook, then the original devs could either do the exact same thing, or make the changes to the .exe themselves easily enough.
EDIT: Now stuff like new UI, updating the framework, etc... yeah, that's a lot of work... but borderless window? Nope. If you can inject the code to make it work with an API hook, the original developer could do it just as easily. Keep in mind the windower team probably had to reverse compile the code to even know what to inject in the first place, while the original devs have access to the source code. Edited, Feb 15th 2017 1:23pm by Lyrailis