The current trend for automation in ArcGIS Pro is to use the .NET SDK for manipulating records, and Geoprocessing tools to create and modify schema. However, unless I'm just not seeing it, at this point there is no toolset for creating and manipulating annotation feature classes (e.g. adding/dropping/altering annotation classes). Working with symbols is a challenge, I know.
In the workflow I have in mind, I'm exporting datasets from an enterprise GDB to a file GDB and massaging them to make them compatible with MMPK creation. I recently ran into an ArcGIS Runtime 100.8 bug that can't handle the HSL symbol colors in an annotation class, and I'd like to find a workaround that doesn't involve modifying the original source schema.