So, I figured I’d comment again here to document where I went wrong. Yes, SURPRISE! This was ultimately my fault 
First, some background
Yeah, this issue goes back a bit.
When YAML automations and scripts first started being discouraged in favour of GUI-based editing, I had a folder hierarchy of a few dozen YAML files that I imported with a packages directive in my configuration.yaml
Importing the new GUI editor files automations.yaml and scripts.yaml didn’t play nice with my existing packages statement. To fix this issue, I added files in the packages directory that imported the GUI -created files in the root config folder.
The problem with my scenes
All that stuff described above was done before scenes were a thing, and I had never created a scenes.yaml import. So while the scenes.yaml file was being written to with the new scenes, it was never being loaded.
Adding a new file scenes_gui.yaml in my packages folder (that was already being included) with this one line fixed my problem;
scene: !include /config/scenes.yaml
Hopefully this can help someone else.
Edit: fixed mistake