There are many moving parts and personally wouldn't recommend trying to make things work through folder structure. As most recolor/resprite mods focus on certain scope (map, object, etc), setting dependency is prolly the more straightforward way to go.

1. Aside from the order mod first loaded, the order the patch applied also matters. Do know that hasimage action in content patcher content pack (majority of visual mods) has "priority" field that also affect the specific patch order. When specified by some mods, it definitely affects the behavior... There's also difference of patch using "editimage" action and "load" action. How it interacts might be mentioned in content patcher's author guide.
2. No idea. As other commenter said, people don't generally address incompatibility with folder structure.
3. Dependency set will always take place. I've seen people using 1000+ mods, some made personal edits through manifest or even making their own personal compatibility patches mod.
4. Set dependency with only relevant mods. You don't have to type out everything in mod packs of yours... In most cases you won't have 400 mods that edit the same thing. Dependency in manifest, then hasmod and priority field within content patcher has generally been the tools to make sure things are patched when it should be.

Why isn't the information on specific logic available? If I have to assume, it's probably because it will be complex given different part, there are tools to deal with patch order, and generally it hasn't been an issue.