It turns out this is a shortcoming on Microsoft's side. It is a known issue that Xbox One Elite Controllers can simply stop working in games for no apparent reason whatsoever. The controller works just fine in Windows 10 and joy.cpl, but it fails to work in games in general.
I'm not sure if this has to do with any controller updates (seeing as there are none, Windows 10 has the latest Xbox One (Elite) Controller drivers built-in, rather it would seem this is due to a, as far as anyone can tell, random change drivers.
!POTENTIAL FIX!
I fixed my controller by going into
Device Manager > Xbox Peripherals,
right click on Microsoft Xbox One Controller and choose update drivers,
and from there choose to browse for drivers manually.
Then select "let me choose from a list of drivers",
untick "show compatible hardware" and select Xbox Elite Controller.
For some reason it was set to "Xbox One Controller" which is completely wrong. This change made my controller start working again.
The frustrating thing about this whole ordeal is that the controller worked just before I started playing Inquisition again so I just assumed it was working with all other games. and so I blamed this on BioWare. Strange thing is, Origin or Inquisition were the only things I updated/changed and I have a hard time believing any of those would incite this change in hardware drivers.
I hope this helps any stragglers looking through this thread for a solution to this problem. It might not work for everyone, but it appears to be working for quite a few.
My apologies for coming across as salty in my previous post, but the frustration was real 😛