I mainly use audacity as an advanced view on my sound files. In my experience the pop-up gets in the way of my work flow when opening many files.
For me it would be logical if on opening I would be prompted whether I want to open the file read only. If so, the pop-up could be disabled for read-only projects/files.
I found a better way to do this in Windows in case anyone is interested, by creating a shorcut on your desktop to do it for you, just right click on Windows desktop then New > Shorcut and set its target to:
taskkill.exe /f /fi "WINDOWTITLE eq audacity*"
There must be a way to do the same in mac with AppleScript, look it up in superuser dot com or similar.