Bot Accounts have been a rampant issue that is being addressed as of late, and their necessity to Content Creators makes them a tricky thing to address.
My suggestion is to allow Creators Affiliate and above to submit Bot Account applications. This would solve a few challenges:
By not allowing less than an Affiliate to create the account, individuals who would create them for trolling would have to actually spend time completing the path to affiliate in order to even create one. New creators would of course need to use the built in Twitch Moderator, but once you become an Affiliate, the rest would come. It shows that you are serious about content creation early on as well.
If someone who was an affiliate went off the rails and decided to be villainous with their bot, it would be tied to their primary stream account, so they would be held responsible for the bot's actions
Bots registered to a streamer would have access to all of the channel's emotes, without having to gift the bot a sub or reaching out to Twitch to get it perma-subbed, as this would happen in the application process. This is a big deal for streamers who want to integrate their emotes into their bot commands.
Technically, people can create main accounts as bots, but with a registration system as explained above, the bots would be easier to filter out and delete, especially in combination with reports from Streamers and their Moderators, and whatever systems Twitch has in place to recognize bots to begin with. As reports come in, accounts flag.
This also protects Creator's bots, since a bot on the channel is not likely to be reported by the Creator's community, and if it is, it would be an investigation of the channel anyway, just like when a creator is reported for all around badness and villainy. (Your robots are not exempt from trial, tyrants.)
For external sources utilizing bots (StreamAchievements for example), they would just have to reach out and apply create a bot account to represent their website. It also gives them something of an advertising page for people to link to and see what their Stream tool is all about.
This covers the gist of the suggestion. Please feel free to reach out for any questions or scenarios in which this would need improvement, and I would be delighted to assist. (In the ideas category, I am not a programmer, just a humble Content Creator trying to make the Twitch World a better place.)
Apologies if this is not the right section for this. I couldn't quite decide on where best to place this.