How can the Panels IPE "add content" modal be customized?
You can do that for all panels pages from
admin/structure/panels/settings/panel-page



Also if you use panelizer you can customize what appear in IPE for every content type.
admin/structure/types/manage/[content-type]/panelizer

Also you can install panopoly_magic module without other panopoly features, only the module "panopoly_magic.info" since it does not deponent on any thing in panopoly distribution.