It just occurred to me, today, that there are no controls to play, pause or stop playback of USB audio: The only options are to lower the volume or power-down the audio system. If USB is selected as the audio source it begins playing automatically when the audio system boots. (I like to keep a USB drive full of music in the non-Android-Auto port for when radio reception is poor or I've just finished listening to an audiobook on my phone - I'm not a Sirius subscriber.) Seems like an odd omission...
Yes I see it as a design flaw. As you noted the only way to "pause" the music is to shut the audio system down which I believe would shut down phone calls too (not sure about that).
Switch to radio. Does that have what you need? I've not looked at controls for the radio, but if it has the functions you want use them and then switch back to USB.
This is the trick I use with my 2016 pilot. If I shut the car down while playing from USB, it starts with the first track when I restart. It is painfully irritating!! I make it a point to switch to FM before shutting down. I kick myself every time I forget. I just got my Clarity and am disappointed it is still not fixed....
At least it's not like the Pilot that restarts the music on the first track. The Clarity will pick up in the same spot in the song that was playing when you shut the car off or switch to another input source and then come back. My biggest gripe is that it takes so looooooong for it to start playing from USB when you first start the car. That and not having a way to pause the music—only skip songs.