Thank you @xangold for your answer!
My use-case is a bot that allow you to play a one-on-one RPG-like game against other watchers in the same channel as you, or against bot-controlled monsters. The battle system is real-time, which means that for an actively fighting player, I’m looking at ~10 whisp per minute from the bot to this player. This means that even if I manage to dodge the whisper_limit_per_sec limit by queuing my whisps smartly, I won’t be able to support more than ~10 simultaneous players under the current whisper_limit_per_min limitations. This is way too low for someone operating a studio called LittleBigMMO 
Ideally, I’d like to be able to enroll in a partner developer program that would lift all rate limitations on both the regular chat and whisper system (and maybe the web API ?), but would be subject to manual approval and then periodic scrutiny to avoid abuse. I think such system would be very beneficial to nurture the growing ecosystem around Twitch features, while avoiding to resort to ugly hacks such as opening thousands of TCP connections in order to support bot on many channels or huge channels. I remember there is already some manual validation for some features (I had to sign a agreement for integrating the streaming SDK in my game Gangs of Space for example…).
Not-so-ideally I could live with the whisper rate limiting being enforced “by connection” instead of “by account”, like it is currently done in the regular chat.