I was around around then, and definitely recall the conventional wisdom being "don't call them URLs anymore, call them URIs, that's the new standard." At any rate, rfc3686 claimed to be a new standard for _syntax_ -- according to the passage you quote, whether it's a "URL" or a non-URL URI is not a matter of syntax at all. The syntax spec is now called "URI". That rfc claims.
Except somehow the result has been just massive confusion over what standard should be used how for syntax of URLs/URIs, with the WHATWG just stirring the pot further (obligatory reference to xkcd there's too many standards let's create another). I don't know that there's anything wrong or to blame in the written text of rfc3986, but something in the social practice of rfc standards as manifested in URL/URI-related things, has resulted in massive confusion and a situation described in OP where there is effectively no formal standard for URLs/URIs consistently used across software.
> The term URL was later changed to become URI, Uniform Resource Identifiers
rfc3986:
> A URI can be further classified as a locator, a name, or both. The term "Uniform Resource Locator" (URL) refers to the subset of URIs that, in addition to identifying a resource, provide a means of locating the resource by describing its primary access mechanism
Personally, I don't treat errors like that as massively damaging to the credibility of the rest of the article, but it is rather jarring, and I know that people do post "Stopped reading at..." comment about this sort of thing.