The docs include info on whispers because theoretically it’s possible to whisper, but there’s so many restrictions, and spam bot prevention measures that aren’t disclosed in the docs, that it’s simply not a reliable system for bots to use as they are more likely for a whisper to fail than for it to be successful.
Because of that, the recommendation who’ve been working with bots on Twitch for years has always been to use other methods of communication. For example for chat bot, use chat. For bots that integrate with Extensions, use that to send data to specific users, or for some other use cases the best solution may be an off-site solution. Whispers are not recommended for bot usage, and if you try to use them then you’ll continue to run issues and there’s no avoiding that.