If mariabackup is executed with the following options:
and "path_to/my.cnf" switches on binary logs, then it will create binary logs in the directory, pointed out in "log-bin" option. If "path_to/my.cnf" is also used by the server, such behaviour can cause issues.
The general issue is if "--export" mariabackup option is used, mariabackup starts the server in bootstrap mode to generate *.cfg files for the certain innodb tables. The started instance of the server reads options from the file, pointed out in "--defaults-file" mariabackup option.