I think this is because the intent of installing the linux metapackage
as described here:

1171                 # If the package depends on dkms
1172                 # we need to install the correct linux metapackage
1173                 # so that users get the latest headers
1174                 if 'dkms' in pkg.candidate.record['Depends']:
1175                     linux_meta = detect.get_linux(self.apt_cache)
1176                     if (linux_meta and
1177                         linux_meta not in self.driver_changes):
1178                         # Install the linux metapackage
1179                         
self.driver_changes.append(self.apt_cache[linux_meta])

Is not honored if the package is already installed:

1048     def on_driver_changes_apply(self, button):
1049 
1050         installs = []
1051         removals = []
1052 
1053         for pkg in self.driver_changes:
1054             if pkg.is_installed:
1055                 removals.append(pkg.shortname)
1056             else:
1057                 installs.append(pkg.shortname)

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https://bugs.launchpad.net/bugs/1506169

Title:
  fresh install - linux-headers-generic linux-image-generic python-
  notify thermald can be auto removed

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