Not able to override config.toml while invoking codex

What version of Codex CLI is running?

v0.106

What subscription do you have?

Enterprise

Which model were you using?

gpt-5.3

What platform is your computer?

MacOS

What terminal emulator and version are you using (if applicable)?

iTerm2

What issue are you seeing?

MCP section present in your repo's config.toml is not overridable through codex --config unless that MCP server is also present in your ~/.codex/config.toml.

What steps can reproduce the bug?

1. In your repo's config.toml

[mcp_servers.sentry]
url = "https://mcp.sentry.dev/mcp"
enabled = false

1. Invoke codex --config mcp_servers.sentry.enaled=true
2. It fails with Error loading config.toml: invalid transport in mcp_servers.sentry

If the same section is also in your ~/.codex/config.toml, the override works.

What is the expected behavior?

_No response_

Additional information

_No response_