Yes, the instructions on the Chapbook website are for adding it to Twine 2. Tee-Wee is a different application, that works differently. You need to first download the format, then load it using the Format button, then Publish. In fact the latter should stop after warning you there's no format loaded; if it doesn't, that's a bug. I'll look into it.
Edit: looks like I misread. Frankly, I've no idea what's going on there. Looks like Tee-Wee did load the format straight from the site (somehow), but when you published the game it actually just saved the raw data?! Just try downloading the story format and loading it from disc like it's supposed to work.