The probe is looking at the log size as a logical unit, not as separate files.
Here is details about the QOS_SQLSERVER_logfile_usage metric:
The QOS_SQLSERVER_logfile_usage Monitors the amount of free space in the transaction log in percentage. If there is at least one transaction log file with "unlimited" growth in a database, the space in the transaction log is considered 100 percent free. Note: For this checkpoint, wherever the given database is in the recovery or restore mode, no metric values would be reported for a given interval of execution.