Those will be used anytime IC2 uses the CLI, but there are times when it won't as an optimization. This includes times when it can use the Tooling API and also times when it can use the Metadata API directly instead of having to use the CLI. The former can be explicitly disabled in
Illuminated Cloud | Configure Application | Validation and Deployment; the latter cannot currently be disabled, though. If you'd like to see an option to disable any direct deployment via the API, please feel free to log an enhancement request in the
public issue tracker and I'll be happy to take a look.
Regards,
Scott Wells