Hello,
If you refer to this article; it states the following for the Automatic Backup method:
Automatic - Backup up transaction log if enabled and then back up database changes since the last full or incremental.
This option lets you back up the entire SQL instance even though some databases may not support log backups. All of the databases are backed up using the Incremental (block level) backup method. In addition, the databases that support log backups are backed up using the Log backup method.
As stated above, the database that support log backups are backed up using Log Backup Method. The Log Backup Method should do the work of truncating the transaction logs.
You may also note that it is normal for the SQL transaction log files to remain the same size even after they have been truncated. The truncate function only increases the free space in the log file to allow SQL to reuse that space vs creating a new log file. Please refer to the following articles to get more details on it:
After performing a SQL Log file backups, the Transaction Log file does not appear to get truncated and the file size does not decrease.
After performing "Log - Backup Transaction Log" of SQL databases using Backup Exec, the size of the physical log file remains unchanged.