Can someone explain how a system container is more secure than an application container, if that is indeed the case?
The article is pretty useless at explaining the difference, I agree. It makes claims about Docker that aren't true (e.g. single container) while making inadequate reference to the OS features likely involved in making "system containers" what they are (SECCOMP, capabilities, network namespaces, nftables). As an engineer this page has a real "trust me bro" feel to it. Maybe fine as a marketing and product positioning…
As a stack, Incus has been exceptional, it has largely replaced Proxmox and Podman Quadlets for me. For context, I homelab so I cannot generalize my claim to SMB or enterprise.
But the documentation has been very end user oriented, information regarding specifics like seccomp as you mentioned are only discoverable with the search bar and that leads to various disparate locations; and that also isn't taking into account that some of the more nitty gritty information isn't on the Incus portion of linuxcontainers.org, see the LXC Security page for example: https://linuxcontainers.org/lxc/security/