So does a renderer such as RenderMan use a baked format like Alembic or a format like USD?
The overall description of the scene, where the desk is, the lights and materials etc, could be stored in a USD scene.
Some tool would read this and generate an intermediate file in RIB format. This would be what a RenderMan renderer actually reads.
For the fluid sim itself, the generated RIB file might contain a reference to a plugin which points to the baked Alembic data, which would be a directory with one alembic file per-frame of mesh data representing the fluid surface.
RenderMan uses RIB files for its scene description and RIB files contain geometry. This means that one RIB file would typically contain a frame of data and source the shaders and textures from separate file paths.