I was able to find a workaround. I simply check if the current URL contains the Beaver Builder suffix (?fl_builder) and in that case don’t load the plugin on this page.
Open wp-external-links.php and change line 24 to this:
if ( ! function_exists( 'wpel_init' ) && strpos($_SERVER['REQUEST_URI'], "?fl_builder") === false ):
It has to be applied after every update, but that shouldn’t be that big of a deal.