IVF is a much simpler format to work with than WebM, so it is used in the example code. The intent of the examples is to show how to call the library, which is independent of what you choose to do with the compressed data once you get it back, and to be self contained, so that you can see the entire code in one file. IVF is what we used at launch. When support for WebM writing was added recently, it wasn't added into the examples mostly because the webm writer was imported in several files, which would break the self-contained nature of the examples.
The vpxenc.c file is a more fully featured encoder than simple_encoder.c, and it has the code for writing webm in it. It should be fairly simple to pull the webm writing code out to put into your application. Search for 'write_webm'.
If you're looking to script command line tools to create a webm from a series of images, then there are certainly easier ways. If you need to do it in C, then you're on the right track.