I'm trying to use the remote GitHub MCP server (https://api.githubcopilot.com/mcp/) with a custom OAuth app in Claude Desktop, following guidance from Anthropic support that this should be possible for servers that don't support Dynamic Client Registration.

Setup:

• Using Claude Desktop with custom OAuth app (client ID + secret)
• OAuth app is approved at organization level
• Token has repo and read:org scopes
• Organization shows as authorized
• GitHub Enterprise with Managed Users (EMU)

Current behavior:

• Can successfully access personal private repositories
• Cannot see any organizations or organization repositories
• When asking Claude to list organizations or teams, it returns none

Question:
Is there additional configuration needed for the remote MCP server to properly access organization repositories when using custom OAuth app credentials? Or does the remote server only support organization access through its built-in OAuth flow or PAT authentication?

The OAuth flow completes successfully with all requested scopes granted, but the MCP server appears unable to access organization data despite the token having the necessary permissions.

Screenshot of Oauth App permissions in the EMU org I want to interact with:

Screenshot of approved Oauth App in the same EMU org:

Thanks!