There's a concept of "separate works", see for example https://www.gnu.org/licenses/gpl-faq.html#GPLCompatInstaller .

Tangentially, I assumed that the GPL must have some built-in exception for running non-GPL userspace programs on top of a GPLed kernel (similar to the System Library exception). However, it seems like it doesn't, since the Linux kernel has its own exception to allow this: https://spdx.org/licenses/Linux-syscall-note.html.

Note that the Linux syscall exemption is actually not the license of the entirety of Linux, because most code contributed to Linux is under the standard GPLv2. It's just a red herring -- there is no need for such an exemption because the generally held view is that such programs are not derived works of Linux (from a copyright law perspective) in the first place.