Hi,
Not sure what you mean backup does not work well, i had seen customer using multiple backup solution to protect workload on Nutanix cluster no matter what hypervisor (ESXi, AHV, Hyper-V).
Yes Protection Domains can be use to replicate the VMs to Single Node Storage Target as backup or Any other Nutanix storage heavy node cluster. It does granular restore using SSR where admin or user can mount the previous snapshots as drive / mount point and copy / restore files.
Using NGT you can use pre/post scripts.
No, as PD is AOS feature it cannot be use on external context.
Now if you are using VMware vSphere you can use any backup solution supporting VMware vSphere, if you are using Nutanix AHV as hypervisor, i will advise to have look at HYCU which is purpose build for AHV or any major backup solutions like Commvault, Veeam, Rubrik, Cohesity, to name few.
If you face any particular issues while testing, do post it here.
F>P