Actually, I managed to add support for Scribe notebooks that use multiple templates. It turned out to be a small change, but maybe a bit hacky:
https://github.com/kluyg/calibre-kfx...64804f757e0fbc
I wonder what the proper fix from jhowell would look like. In the meantime, if you can't wait, I'm attaching version 2.12.1 which supports Kindle Scribe notebooks with per page templates.