It is possible to replace MySQL with MariaDB; however, you should not do so unless you are an experienced system administrator.
Check the MariaDB documentation and contact MariaDB support for assistance.
If MariaDB is installed correctly, it should not cause any issues with ServerPilot or autoupdates.
If you intend to continue using ServerPilot to manage the server's databases, you must make sure all existing MySQL user permissions are retained when you install MariaDB. If the existing permissions are lost, ServerPilot will not be able to manage the server's databases.