Quote:
When I click the polygon tool again I do not get a message box asking for
confirmation to apply transparency?
I think it's automatic. Once you have completed the georefencing points and click "Convert to UTM", the polygon mask will be applied during the conversion.
(With a USGS GeoPDF source, where TransDEM recognizes the projection, you don't enter georeferencing points, of course, and go straight to "Convert to UTM" after clicking the polygon mask tool the second time - and the margin has become semi-transparent.)
The behavior may been slightly different in earlier versions of TransDEM, but I am not sure.