I had thought there was a way to include attributes on the tags when you add them to the HTML Include Filter config option but looking at the code I don't see it (plus it is not mentioned in the docs).
So 2 options for you now until we get this fixed.
You can either enable Skip Filtering for Admin config option found just below the filter config options.
Or download the autotag plugin and enable the youtube autotag.
Autotags Plugin v1.1.3
The autotag plugin is really handy. Plus using it for youtube will allow you to style it in one spot but use the code in multiple places on your website. I have an update to the youtube autotag if you want it which gives you much more control on how it looks.
This has the added benefit of security since ideally you don't want regular users usually to be able to create an iframe on a site.
By the way I added a bug for this issue on GItHub
https://github.com/Geeklog-Core/geeklog/issues/1078
One of the Geeklog Core Developers.