I have been investigating the issue for a couple of days, the only legal way to modify filters, range of dates, etc in iframe embedded in my application is through the URL.
But that is a pain in the ass, besides, it means having to add an extra widget in my app to manipulate the URL of the Iframe ... a crap.
By the way, Kibana uses Rison to encode and decode that URL to JS object, I'll leave it here if it's useful.
Peeero, after analyzing the Jib of Kibana I realized that they are simply hiding the filter bar when Kibana is in embedded mode, you can modify the code of the application so that it does not. For Kibana 5.4.1
I recommend that you take a look at /optimize/bundles/kibana.bundle.js