I had the same problem and was able to resolve hooking into pum_popup_content and filtering out empty lines, comments, and empty p tags. Drop this into your functions.php or plugin:
/**
* Fix for Popup Maker Gutenberg compatibility
* Need to strip out comments, blank lines and empty paragraph tags
*/
add_filter( 'pum_popup_content', 'veer_popup_maker_gutenburg_compat' );
function veer_popup_maker_gutenburg_compat($content) {
$content = preg_replace('!/\*.*?\*/!s', '', $content); // empty lines
$content = preg_replace('/<!--(.|\s)*?-->/', '', $content); // block editor comments
$content = preg_replace('/<p[^>]*><\\/p[^>]*>/', '', $content); // empty p tags
return $content;
}
Note that pum_popup_content only runs when a popup is saved/updated. So to see the change, you’ll need to click update since the popups are cached.
Hopefully this saves someone out there some time!