Just because Transmageddon / gstreamer has loaded your va-api driver doesn't mean its being used and in your case it won't be getting used because you have transcoded to ogg.
To encode in a format that should use vaapi, choose AVI for the output format then it should choose h264 as the default codec.
However, there is no point in trying unless you have the required gstreamer encoding plugins. What distro are you running and what output do you get when you run:
Also, make sure you are running at least Transmageddon 1.3. It seems your previous test used 1.2 and 1.3 fixed a bug that disabled vaapi.
gst-inspect-1.0 | grep vaapi