Hey MathematicalTea, welcome to the forums.
Almost all of those unofficial fixes apply to your copy of the game data. This isn't something I need to do with Daggerfall Unity because it connects to your install of the game and uses that same data.
So if your copy of Daggerfall's game data is patched, then Daggerfall Unity is patched as well as far as that data goes. I have other new bugs all of my own.
I always recommend people use the DaggerfallSetup installer which installs all those key game data fixes for you.
Quests (which are decompiled and included with Daggerfall Unity) have all the available quest fixes applied. They still have lots of bugs even then. Fortunately it's easier than ever to fix quests as they're now just a plain text file that is compiled at runtime.
For the other mods, some of them can work with Daggerfall Unity (those that swap textures and text for example), but your mileage may vary. Under the hood, Daggerfall Unity has a whole new engine and a different way of doing things, so any compatibility with high content mods like Werefall, etc. would have to be recreated. It would be interesting to see one day though.