It's not easy to run the Converter in WinPE environment, generally you need to copy installation on WinPE and correct paths and registry, Converter should run after that.
But running Converter in this way will copy WinPE OS not your real OS, as result your VM probably will not run.
Are look at 'Data to copy/Advanced' options? There are ability to change and exclude volumes, I don't understand "Converter doesn't give the ability to choose which Windows partition installation to modify on the source server, to change drivers or anything else."
The open files are not a problem for Converter because it uses VSS, for changed files during conversion there is a 'Incremental' option.
HTH