No, one should probably never use unregistered suffixes. But that’s not to say that all DNS names should be public, nor that NAT is practically avoidable, so this is beside the point.

What one should do is only choose DNS servers capable of properly resolving all addresses, as it shouldn’t be the resolver’s responsibility to “shop around” for answers.

Fixing VPN configurations that complicate this should be the responsibility of VPN client software — by providing a forwarding DNS server that falls back to the originally configured servers, say — not the resolver, and similarly for any other cases where standard resolver behavior does not suffice.

Application software, for its part, shouldn’t generally rely on implementation-defined resolver behavior, as doing so is obviously not portable, but that’s less sinful than a VPN relying on client library-level support to work around the fact that it’s exposing a broken network configuration.

Note that I have no axe to grind one way or another in the systemd debate: Linux isn’t me primary OS, but I regularly use and abuse both systemd and non-systemd Linux systems, and all the Linux init systems seem to work at least as well as any other system I regularly use (OS X, FreeBSD, Windows) for most practical purposes.