I like the darker panel more. The idea behind a plain black panel for Adwaita is that it blends into the monitor’s bezels. The top panel should be something thats fades into the background when you’re not interacting with it. I don’t think it needs too much highlighting.
In the following mockups, I removed the panel shadow since it made the titlebar of maximized programs look too blurry and replaced it with a black border ( which is more obvious depending on the wallpaper or when a window is maximized). I kept the panel at #181818 with an alpha value of .95. The dash is the same color but the alpha value is 0.90 instead.
When a window is maximized the dash stays the same and the panel becomes opaque. You can see the black border separating the headerbar from the panel. I used a box-shadow here as a border would make the panel 1px taller.
I find that without the borders and with a lower contrast background (your example here uses a much lighter background color) that the button blends into the background too much. The buttons also look much darker than in your example. I’ll play around with a lighter color because while I do get your worries about too high contrast I also don’t want things to look dingy.
The top right corner only shows system and app indicators, there’s no way to insert the Ubuntu logo there. In contrast to the wifi, bluetooth and other indicators it’ll just be a passive icon, too. It won’t be best place to put it.