Windchill is flexible enough to allow the modification of OOTB routing workflows and the creation of new routing workflows, but there's no flexibility in implementing these routing workflows. If a new routing workflow is created, it will show up in all projects and there is no functionality to limit the available choices at the project level.
If I make a new workflow for a single project and deploy it, it is deployed to all projects.
If I remove any existing workflows, they are removed from all projects.
I want to make things simple for my users by providing only the choices that are relevant to their project. PTC should add the ability to configure which routing workflows are available for each project and for each container if they ever extend routing to products and libraries.