Defined in / Last changed by "Unknown" indicates the entity was not statically defined or overridden by a plugin, but was dynamically created or modified at runtime, by a Papyrus script, or by the engine itself. Or possibly by a SKSE plugin (such as Base Object Swapper) but I'm not sure about that.
MIC has some bugs where it erroneously reports "Unknown" in some cases while it should not, but according to the MIC MA it only affects NPCs.
You can always tell an entity was created at runtime because the load order index of its Form ID is FF. Hence there can only be up to 253 "fat" plugins in the load order: index 00 is Skyrim.esm, index FE is reserved for "light" plugins, and index FF is reserved for the engine. 256 max theoretical limit - 3 always reserved = 253 available.
In any case, the engine is completely oblivious to overwritten DDS texture files or NIF mesh files, so changing the overwrite order of those files cannot be detected by the console and reported as "Unknown". If you're seeing "Unknown", it's caused by something else.