If you deploy XPenology as a VM then you can work around hardware that would otherwise be incompatible or less compatible as baremetal. For example, I can use my enterprise NVMe disks as regular storage (a disk pool and volume), and also RAID F1 which is only supported in DS3615/17xs, both at the same time deployed as a ESXi VM.
If you have a need for other VM's and they do not need very high speed access to DSM volumes (meaning they can be NFS connected or even use hypervisor storage), then arguably ESXi is a better pure hypervisor instead of a container inside DSM.