I'm a bit skeptical about the performance penalty. I know there's a benchmark but I didn't see any details of what was actually benchmarked and where. Windows (AFAIK) still has notoriously slow directory traversal operations. God forbid you're using SSHFS or even NFS. I've seen things with hundreds of YAML nodes before.
Benchmarking this is also tricky because the OS file cache will almost certainly make the second time faster than the first (and probably by a lot).
Also just the usability... I think opening a file to change one value is extreme. You also still have the problem of documentation... Which sure you can solve by putting that in another file, but... You can also do that with just plain old JSON.
I think in the majority of languages, writing a library to process these files would also be more complicated than writing a JSON parser or using an existing library.
Also how do you handle trailing whitespace inserted by a text editor? Do you drop it? Keep it? It probably doesn't matter as long as the configuration is just for a particular program. The program just needs to document it... But then you've got ambiguities between programs that you just don't have to worry about with TOML or JSON.