Secure boot, as the name suggests, secures initial loading of the most central/core parts of an operating system: (indeed) the kernel and kernel modules.

While APTs can be installed on different levels, anywhere from kernel up to user space, a good (hard to detect) place for those is inside the kernel itself or in a kernel module.

Secure boot is definitely intended to prevent APTs, even if its only a part of the the full equation. You still need additional tools on top of a kernel, e.g. SELinux or AppArmor, that monitor, audit and (hopefully) prevent the introduction of APTs. However, without a trusted kernel (and kernel modules), all of those tools can be compromised/circumvented, making it ultimately an impossible task to secure the system as a whole.