You can just ignore the new plug-in management options and continue using the Plug-In Manager. All the custom layouts I created previously, even those with subfolder within nested folders, open up just fine.
I also did a test just to make sure you can still create custom layouts with sub-folders using the Plug-In Manager, and you can.
After an initial period of disorientation I'm going with the new approach, but that may be because it's congruent with my workflow.