@ was used for documentation but v2 has its own documentation field. Are you thinking of some note-making use case distinct from documentation? `"doc": "blah blah (note: bleh)" seems simpler.

@ was used for documentation but v2 has its own documentation field

For configs, but not for top scope IIRC. In any case, docs about specific value and docs about config sections (such as "the configs below deal with fulltext search profiles") can be different.

Are you thinking of some note-making use case distinct from documentation

Well, I can live without notes in docs, as long as notes outside docs work, I guess, though it's a bit confusing - in v1, @note worked in both places, in v2 @note works only in one place, despite what the docs say. So I'd like to figure out what it would be going forward and if @note in configs is not going to be supported anymore, it should be clearly stated in Mediawiki as no longer recommended way to do docs.

Well, it's definitely not the recommended way. The doc property can be introspected and internationalized and will eventually be exposed on some admin interface.