VirtualBox is capable of running on multiple platforms and handling different kinds of virtual disk formats, including VMware VMDK files that are used for virtual machines hosted in VMware ...

Programmatically, I'm not sure. But in Windows you can associate a drive letter to a disk number, then out in VMware you can associate a disk number to a VMDK filename.

The boilerplate answer is to shrink the VMDK... but these Linux VMs use an ext4 filesystem, which VMware does not support shrinking with their conventional tools (i.e. vmware-toolbox).