[Mosu]

Sure it can. On the merge tool go to the »output« tab. On the lower right you'll see »additional options«. Either enter the option manually or hit the button to the right of it which will open a dialog showing all available additional options. In that dialog you can also opt to have the selected options be set for each new merge job by default.

You can find the same default options in the preferences dialog on the »merging« tab. Here it's called »Default additional command line options« with the same button and the same dialog attached to it.