Great write-up!
It’s good to note that the tools you setup for a project in its anatomy settings I believe are the default tools for a new asset. Existing assets in a project will not automatically get those tools assigned.
This might differ if using a project manager like Ftrack which might push attributes in a different way but the active tools are stored in the database per asset if I’m correct. So that you can even differ the version of a tool per asset or shot. The Project Manager tool in the Launcher for example does not automatically propagate the tools from the project to the assets.
So where available Applications are defined per project, the available Tools are defined per asset/shot. (Even though on a project level it does allow to set which tools are allowed to be set in the project)
By the way, you should update your Yeti label, Pergrine Labs → Peregrine Labs