Yes, if you add .me to messages it will become a nickname message on Twitch which will give it the coloured message. I agree having a checkbox for making a message a nickname message would be beneficial in the long run as you won't need to keep typing .me every time you create a new command. As for each message that Deepbot sends I don't know if this would be the wisest idea in the long run. Unless your bots chosen colour on twitch is legible on both the default and BTTV Dark colour scheme it could be difficult for some users to read specific messages from your bot.
Feel free to make a topic in feature requests though to gauge how interested Deepbot users would be in this. I can't see any harm in adding the option in. I would also suggest adding in the ability to change the bots user colour in that list of options so you can change the bots message colour on the fly.
Thanks,
Dante557