That's a very nice post! I was wondering how it worked myself not long ago, so it's spot on for me!
As you seems knowledgeable in Unity (I only knows UE4 myself, and that's more or less only for 3D works in the graphics department), is the structure of having large packed files is an absolute necessity, or even by-product, of working with unity?
Can't you have just every files that are packed not packed the old-school way and put into different folders? This would make navigating through the files and modding so much easier, and most of all, would make mods traceable by allowing JSGME!
I can foresee the inevitable CTDs, but it's going to work a la GTA5 I guess. Mind you, we don't know what will be in the SDK yet, so... I guess it's the good way to work in the meantime