Comment 4 for bug 1787460

So, this might partially be a linux-meta/overrides bug. The top-level metas (linux-$flavour) should be in the metapackages section so that if they're removed (for instance, by someone who doesn't want headers, but kinda likes kernels), the manually installed bit is transferred down one level to linux-image-$flavour and linux-headers-$flavour.

It might also be valid to say that the neverautoremove apt/kernel magic could/should include the mid-level metas in the list, so they're just considered manual regardless of what state they were accidentally put in.