The Dark Souls 3 profile is part of the source code same as Nier and a few others though less extensive mods but later versions of SpecialK including DS3T / Souls Unsqueezed itself have a chance or are almost guaranteed to hit the soft ban state of being blocked from the common multiplayer space and activities from other players and will only see activity from others that are also soft banned.
I don’t think appeals work for third party utilities such as SpecialK either.
So that’s the main drawback.
Config wise if it’s not using a secondary ini file the categories should be added to the main config.
[SUS.Display]
HUDResX=
HUDResY=
HUDOffsetX=
HUDOffsetY=
StretchHUD=
[SUS.Render]
DefaultResX=
DefaultResY=
FlipMode=
SacrificialResX=
SacrificialResY=
StartFullscreen=
[SUS.System]
LastKnownAddr=
ShowOSDDisclaimer=
Version=
[SUS.Window]
Borderless=
Center=
Fullscreen=
If there is a secondary ini it should be named SoulsUnsqueezed.ini and it’d likely be in the game folder since I don’t think it would branch off into the user folders like the main SpecialK config does now.
(Older plugin.)
If these don’t do anything at all or seem to work then the mod is not entirely part of SpecialK’s code and like Final Fantasy X, Tales of Zestiria, Berseria and Symphonia you need the stand-alone version for full functionality.
I think Fallout 4 too and then Nier Automata would have been part of this but that project was updated more recently so it now works in the newest version of SpecialK also along with how there’s profiles with game specific defaults and smaller compatibility tweaks or fixes outside of these larger projects. 
(Far as I know that is, not 100% on the state of FAR for Nier Automata.)
EDIT: Dragons Dogma as well, there’s been a few stand-alone fixes and tweaks since the Batman Arkham Knight memory tuneups.
(Monster Hunter World I suppose also qualifies as having a bit more to it than some of the other stuff from the full list.)