Is there any way I can create a Virtual Box disk image (.vdi) that is NTFS formatted and copy a set of files to it prior to attaching it to an already configured instance as a second disk using VBoxManage?
Yes, you will have to:
Ways of doing that are described in this post:
https://serverfault.com/questions/210684/how-do-you-mount-a-vdi-image-on-linux