What would be the advantage of running Nextcloud as a docker, instead of within a VM?
No idea really beyond the usual VM/container trade-offs, I guess it would allow you to use orchestration tools and similar for Docker.
What would be a sensible way to have an incremental/differential backup of the VM/Docker?
If you use Proxmox as your hypervisor it comes with a sophisticated backup solution, probably the same for ESXi or whatever. Not sure about Docker.
The storage usage of my Nextcloud instance exceeds 1TB. If I run it within a VM, I will have to connect it to a 2TB SSD. Does it make sense to add the external storage space to the VM? [...]
That's what I would do at least. Connecting external storage space to a VM/container is relatively trivial and Nextcloud recommends to separate binaries and data directory anyway. Plus this allows you to use different backup strategies for data versus binaries+metadata.
It's basically a collection of three shell scripts to install, manage, and update Nextcloud. Last time I tried it also worked on LXC/LXD, not only VMs. It would probably work on Docker as well and has some files related to that in the migrate/docker directory.