As explained here:
https://docs.opsmanager.mongodb.com/current/tutorial/manage-project-settings/index.html#admin-project-settings

The Ops Manager global admins can override the logLevel setting on a project for Automation and Monitoring Agent modules using the webUI.

This will cause the Agent to override the local config logLevel setting to what's set in the webUI.

Please note that this global admin project setting is redundant as the logLevel of the Agent modules can be also set by using the "Edit custom configuration" window in the project agent settings page as explained here:
https://docs.opsmanager.mongodb.com/current/reference/mongodb-agent-settings/#configuration-file-settings-locations