They're slots for prefabs that are instantiated at runtime. For example, a basic DFTFU scene might use a basic enemy type while the full game uses a heavier serialisable enemy prefab instead.
Check the DaggerfallUnity gameobject inspector in game scene to see the prefabs currently assigned.
It's a fairly common Unity pattern for setting references to prefabs that spawn later (e.g. missiles, particles, mobiles, etc.)
Don't worry, I feel the same way. I learned more about Unity while tooling up the initial systems. For the last couple of years I've been drenched in quest and magic systems which are about 95% divorced from Unity except for a few places they touch the world. I feel my learning has stalled for a while now.