Mac's Preview app displays disabled layers in PDF. Is there a way to workaround it?
Without purchasing Adobe Acrobat Pro, I couldn't find a way of removing the disabled layers from the PDF so that Preview will not get confused.

I was able to find an alternate solution for my end goal of exporting the PDF as an image.

In Acrobat Reader,


Edit > Take a Snapshot (enable)
⌘-A to select the whole page (now Acrobat copies the image to clipboard)
Sometimes have to ⌘-C to copy image


In GIMP or other image editing tool,


Open a blank image for the right size and dpi. For the USGS topo map, it was 24 in x 29 in at 110 dpi (was my default in Acrobat Reader's preferences).
Paste from clipboard.