I also have this exact same issue with the VIVE Pro Eye that I just set up.
I can launch games that I purchased through Steam, and are run through Steam, but whenever I try to launch any game purchased through Viveport I get the device setup pop up, and I have tried all the same things as OP with nothing working for me.
I have run the set ups and install every way I've seen suggested on any threads and help articles I could find, and nothing works.
For now I am just only able to run things through steam.