Can I select something across multiple layers?

[rich2005]

@ Geocide

You have set up nicely What you can do is
Go to the port layer then Layer -> Transparency -> Alpha-to-Selection. That will select all the red block
Go to the above port layer then Layer -> Transparency -> Subtract from Selection. Using that will keep any semi-transparency in the selection.

You can check the effect with a fill: 30 second demo: https://i.imgur.com/iZlsUbM.mp4