Today (-126.96.36.199), there is no way to make the Publication Settings be consistent over the lifetime of an illustration - new Figures do get all of the publishing profiles enabled by default even when the column checkboxes (complete profiles) are unchecked. See screenshot: when profiles are disabled for a Figure, they get re-enabled for new Figures.
A desired behavior for new Figures would be to only “inherit” those that have not been deselected completely (in the column header) in the Publication Settings and/or to be able to set the profiles to include when Saving specifically (as changing some settings for a temporary publication sticks when saving).
We have standards with several profiles for various output, including multiple Creo View publication profiles, and when saving the files with client-side publishing it can take a very long time to complete. Today the workaround for the users is to go to Publication Settings before saving/checking-in any file and that step is often forgotten.
A related improvement would be to bring the whole set of Publication tools and actions up to a higher level, e.g. by having them collected in a “Publication” tab.