How to copy files on new HDD without empty space at the beginning NTFS partition

I wanted to backup files from one hdd to another similar, empty one without fragmentation. I tried using the Windows copy paste method inside windows Explorer, using SyncBack Pro and using Linux.

Windows and SyncBack Pro gave similar results – the files were fragmented (12% fragmentation shown inside Auslogics DisDefrag and O&O Defrag – which is bad), but there was no free space at the beginning of the NTFS partition (which is good, if you want to copy other files afterwards).

Linux gave a different result – the files were not fragmented, but the copy process left empty space at the beginning of the drive, before the location of the first files on the new drive.

Is it possible to copy files on new HDD without empty space at the beginning NTFS partition?

The results:

O&O Defrag results after SyncBack Pro copy

Smart Defrag results after SyncBack Pro copy

Smart Defrag, after using Windows to copy

As you can see in Smart Defrag I get red regions, meaning fragmented files.

Linux copy gives a different result:

Smart Defrag analysis results, after Linux copy using Files(nautilus)

I therefore started a defragmentation using Smart Defrag 6 – free space defragmentation method, and the files are moved to the beginning of the drive.

Smart Defrag, following Linux copy, during free space defragmentation

I want this final result, but directly using a copy methond inside Linux (or Windows – but I don’t think it’s possible).

Smart defrag 6 colors:

Magenta – Directories;

Red – Fragment;

Green – Frequently used;

Yellow – Master File Table;

Light Blue – Unmovable;

I need the partition to be NTFS.

I used a Ubuntu 14.04.6 x86 Live USB stick.

Inside Nautilus I used the default copy paste method.

I had 16 GB RAM and about 2 ssd-s and 3 HDDs connected.

The new drive had one NTFS partition, partitioned in Windows 7.

Thank you for your help.