I'd say the most valuable thing these tools provide is a way to link notes. That's the part that was missing from most of my attempts to build my own knowledge base, creating connections between the things I find and store in a way that's personal to how I think.
In the end, my ZK is nothing but a folder filled with md files that are all linked with each other in some way. It's synced to my phone and my tablets, so I always have them with me and I can always amend or work on them.