Dear Albert,
As Alexey wrote, in the current version of the library (1C:Subsystems Library v. 2.2.4.11), you have to manually locate unnecessary dependencies and get rid of them during the merge.
Please be informed that we are developing a new international version of 1C:Subsystems Library that will be available later this year and will include new functionality and correction of known issues, of course. One of the issues to fix is to ensure that it is possible to merge only three required subsystems ("Base functionality", "Users", and "Infobase version update") from the library into a target configuration according to a simple instruction.
Best regards,
Vladimir