The “Search Preferences” checkboxes apply to only the search for updates.
The “Update Classification Filtering” checkboxes apply to only the download and installation of updates.
When you use ‘Check for available updates’ it will search based only on the “Search Preferences.” This means that you will see all different types of updates listed as available for the target computer. However, if you then go to actually perform the download/installation, only the updates that have the classifications that you have ticked/checked/selected will be downloaded and installed. So if you have ONLY “Security Updates” checked, then only updates with the classification ‘Security Updates’ will be downloaded and installed.