Because rate limits and anti-spam measures are 2 separate things. New accounts have the same rate limit old accounts do, but the anti-spam measures (which Twitch doesn’t disclose for obvious reasons) impact them more than old accounts.
As has been stated many times previously, there are a significant portion of devs who have been doing this for years who have some accounts that can send whispers, and some that can’t, regardless of age or known/verified bot status. If you’ve been lucky enough that you haven’t experienced issues then awesome, but it’s something that’s been warned about on the forums and TwitchDev discord for a long time now so if it’s impacting you now, that’s unfortunate but expected. Perhaps now would be the time for you to look into a solution more fit for purpose than whispers for your bots.
I agree that the docs could be updated to mention that there are other security measures in place to prevent misuse, but the specifics would likely never be included in the docs.