Yes, the white/black list for patching is still there and has been extended. You now create smart groups of hotfixes based on the patches downloaded in the patch catalog. One or more of these can then be assigned to a patch analysis job, so it is now much more flexible and easier to use.
The patch catalogue filters aren't intended to control patch analysis, more to limit the number of patches downloaded.
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The catalog should contain all possible patches you'd want to use, I wouldn't do too much filtering there. Do your filtering w/ the smart groups. So multiple PAJs can use the same catalog, just w/ different smart group filters.