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Currently facets do not show up inside elementor popups. The elementor popup builder provides much more granular control vs the flyout add on. Supporting facets within elementor popups will allow me to create more advanced filtering UI's for my users on templates that have a lot of possible facets to filter by. (especially on mobile where having a ton of filters on the page is a bad UX)
Possible solution:
Doc page: https://developers.elementor.com/elementor-pro-2-7-popup-events/