Most UIs currently are unsophisticated and let you turn on or off the tools on server-by-server basis. For some large servers (especially if they act as aggrgeators) this approach isn't going to be desirable and you are going to want to select individual tools to activate, not servers. But that's a UI issue more than a protocol issue.
We've been thinking that an intermediate (virtual) server layer might be helpful here. Actively working on something to solve that now and looking for feedback, please reach out if interested.
Vscode let's you go tool by tool. It's great