Because json is poorly suited for config files, and it is very convenient to have config files that closely mirror apis, like kubernetes does. I've seen too many teams who try to use json for config end up developing yet another custom superset of json to allow comments or multiline strings or such. If you are going to use a superset of json might as well use an existing one like yaml or json5.

That said I agree with all the criticisms of templating yaml. We have to do the same (with helm and other tools), and I have pushed hard to adopt conventions that we only use flow-style and not block-style to avoid all the white space problems when splicing together chucks of yaml. And on the plus side we get trailing commas and other such niceties which don't exist in json and make it harder template.