I think your starting point (allowing bot user agents to crawl the web has overlooked benefits) is a good one, but things aren't black and white--there are clear drawbacks, too. Bots obviously have an orders of magnitude higher potential for abuse; to the point where bot traffic--as it currently stands in the real world--is qualitatively different from human traffic.

we should expand these protections from intentional/unintentional ddos irrelevant of user agent.

Sure, but targeted regulation based on heuristics (in this case, user agent) is also a widely accepted practice. DUI laws exist, even though the goals (fewer murders and safer roads) are already separately regulated.

Would it be nice if we didn't have to do this? Or there were some other solution? Sure, but I have no idea where to even start, unfortunately.