I consider the inconsistency to be an issue.

I see your point, and it would be an option for URI to include a config option to encode spaces as %20 instead of + in the query. OTOH, I think the reason for the OP asking this question is strange, because it seems that either OP doesn't know that + is a valid encoding for space or there is some other misunderstanding of URIs, or perhaps they're building a workaround for a server that doesn't handle +, which would also be strange, and I might suggest (also) looking into the latter problem.

I would question the relevance of including that entry from almost 22 years ago

It was a reply to your "I don't know if the '%20' vs. '+' issue has always existed, or if it's something that was inadvertently introduced with some change." (Update: Emphasis mine.) A git blame shows the relevant lines of s/ /+/g; have been unchanged for 22 years.

it even references HTML4 which certainly isn't current

As I linked to in my other node, in this instance the HTML5 spec is backwards compatible with HTML4.