For all practical purposes Linux currently has _two_ stable boundaries, libc (glibc) and kernel. If you move it so that the stable boundary is only the kernel, you still have this problem. If you move it so that the stable boundary is only libc, you still have this problem.

In fact, TFA's problem comes from applications passing time_ts around, which is strictly a userspace problem, and the syscall interface is almost entirely ortogonal. Heck, the 32-bit glibc time_t functions probably use the 64-bit time_t syscalls these days...