The boxes will be flush mounted then? I’m having trouble visualizing that…. But if it’s that important to you to fill the conduits, you can use duct seal. In the trade it’s referred to as monkey sh*t. It’s almost like play doe, but thicker.

As far as your HDMI question goes, that really depends on the receiver you use. Some will only pass whatever comes in as HDMI, out HMDI; others will output video with HDMI or Component independent of the input.