It's a fundamental user experience flaw with the MCP server. It does indeed need fixing - e.g. it could have a permissions system itself, so even if the GitHub

It's a fundamental user experience flaw with the MCP server. It does indeed need fixing - e.g. it could have a permissions system itself, so even if the GitHub token has permissions, different projects have their tool calls filtered to reduce access to different repos. Or it could have a clearer UX and instructions and help making multiple tokens for the different use cases. The MCP server could check the token permissions and refuse to run until they're granular.