This is totally possible. The color picker in Astroid let's you select RGBA colors, which means you can add transparency wherever you are selecting a color.
The background color for Astroid header (in this case your menu) is set on the column level. Under Astroid Options Go to >> layout Manager >> Astroid Header and then use the edit icon on the right (element level).
Once inside the popup, click the design tab and click the background color and use the second slider to adjust opacity or directly type in the RGBA color. I did it on the seattle demo to test and got a screenshot before I changed it back.
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