Currently, my main concern with YAML is that, by the spec, comments are not attached to a particular node (see https://yaml.org/spec/1.2/spec.html#id2767100). As a result, a lot of YAML parsers (like https://github.com/yaml/libyaml and https://github.com/chyh1990/yaml-rust) only filter out the comments during the parsing phase. This makes it less than ideal for a use-case where the configuration file is expected to be modified by both programs and humans.
TOML makes it more trivial to associate comments with a node. This is mainly because the language is simpler though, as the spec is not explicit about that (https://toml.io/en/v1.0.0#comment).