You can set MongoDB log rotation for mongod process on project level in the Ops Manager through: Deployment -> More -> MongoDB Log Settings. However there is no option to set it via API.
It looks like there is option to set this parameters on process level (in the Automation Config), but Ops Manager is not accepting new value, like it does when setting values for Monitoring Log rotation and Backup Log rotation.
It would be great to have option to automate this when creating a new project via API and setting all other attributes with script.