I did more tests and apparently the in-game FXAA found in the config is actually SMAA on Ultra, no wonder I was not noticing any difference when I was applying SMAA without disabling FXAA in the config. I thought SMAA was not being applied but that wasn't the case.
With FXAA disabled and no other AA method or injector the game has some serious jaggies (check the roof on the car):
FXAA OFF in config without any other AA method:
FXAA ON in config without any other AA method:
FXAA OFF in config + SMAA injector on Ultra:
As you can tell with FXAA off you can clearly see the game is running without any kind of AA as the jaggies are very noticeable, but when you turn on the in-game FXAA without any other AA and compare it with the screenshot with SMAA on Ultra with FXAA off you can clearly see there is no difference whatsoever.
Also, injecting SMAA on Ultra was taking about 3-5 FPS compared with just FXAA and it's something to keep in mind if you have low FPS or simply can't achieve 60 FPS locked constanly.
SweetFX however still is able to change all of it's settings like sharpness, saturation, etc, except SMAA since it's the same thing.