The Twee2 compiler comes with SugarCube v2.7.0 pre-installed and the StoryInterface special passage was added in v2.18.0, this is why that special passage isn't working with you build and view your HTML file.
note: It is the story format engine that knows what to do with this special passage, the compiler is generally only responsible for embedding the relevant Passages within the story format's template to produce the HTML file. In the case of Twee2 it does interpret some of the contents of specific Passages to determine some of it's own settings.
The following steps describe how you upgrade your version of SugarCube to the latest version.
1. Determine where Twee2 installed it's SugarCube2 story format folder.
You start with using the following (ruby) gem command to location the Twee2 installation...
gem which twee2
... this should result in a file path similar (but not exactly the same) to the following.
C:\Ruby23-x64\lib\ruby\gems\2.3.0\gems\twee2-0.5.0\lib\twee2.rb
... and the part you are interested in is..
C:\Ruby23-x64\lib\ruby\gems\2.3.0\gems\twee2-0.5.0\
The above location should contain a storyFormats folder and within that one you will find the SugarCube2 folder.
2. Download the latest version of SugarCube 2 from the Downloads section of it's site, you want the compiler related release which should be named something like
For Twine 2.2, Twine 2.1, & Tweego (local/offline) [ZIP archive]
Once you have extracted the contents of this archive file onto your local hard-drive you should have a folder with a name like sugarcube-2.25.0-for-twine-2.1-local which in turn should contain a folder named sugarcube-2 and that folder should contain three files named:
format.js
icon.svg
LICENSE
... theses three files are what makes up the story format.
3. Copy the above three files into the SugarCube2 folder you located in step 1, this should overwrite the older v2.7.0 release of SugarCube2 that came with Twee2 with the latest version.
4. You can test that Twee2 is now using the latest SugarCube2 by first adding a StoryInterface special passage like the example in the SugarCube 2 documentation.
:: StoryInterface
<div id="passages"></div>
... and then using a twee2 command like the following to build your HTML file.
twee2 build my-story.tw2 my-story.html --format=SugarCube2
note: Obviously you will need to replace my-game part in the above with the actual name of your TW2 file.
5. Open the resulting HTML file in your text editor and look at the contents of the head element and you should see a comment that includes a line that starts with.
SugarCube (v2.25.0)
... and if you open the HTML file in a web-browser you should see that the standard SugarCube2 User Interface is now missing.