1) Proxies and botnets obscure origin and make attacks appear globally distributed so basic rate limiting has little effect on these attacks.

2) Extrapolated averages on incomplete data are certainly suspect, they are meant to be taken with a grain of salt and are most applicable to people in the affected industries for them to validate against their own data. FWIW The highest percentage of malicious, automated traffic that I've seen has been 99% which, yes, is crazy and should sound unbelievable.

3) Noted, definitely. It is certainly a tough number to nail down because it is very dependent on all the things you mention. I trust our data because we've been at this the longest, were the earliest, and we see a lot of the unadulterated attack traffic that has gotten through many existing defenses so we see the stark difference on day one.

Disclaimer: I contributed to the report in question (but was not consulted or related to the posted article)

I think an important thing is that you should consider that attackers will log in at the maximum rate limit allowed. The traffic may even be greater than the rate limit, and they'll have some requests dropped by the server. But it still represents and attempted login regardless.

So, yes, even with rate limiting, you can still easily hit 99% fradulent attempts. Obviously you'd be foolish to actually process all of those, and likely the attackers would realize they were rate limited and would slow down for their own best interest, but it's not a guarantee that they actually do obey the rate limit.