The link in the readme for installing tombot, I can't help but notice, features a permissions=0 in the query string. I think there is a possibility that if that were otherwise, the bot could have emoji permissions right away by default, as it did when I installed a test version on my test server. I added some permissions by scrolling down on the Developer Portal OAuth2 page and checking their marks like the following:
As you can see, this gave me a URL with a number for the "permissions=", and I think there's half a chance that creating a URL for the real tombot along those lines might obviate emoji-permission-giving hiccups in the future.