Not sure if there are any better ways
Point to a script method:
1) Make a shell script. Presuming that the paths are identical :
__GL_THREADED_OPTIMIZATIONS=1 "/home/andrew/.cxoffice/battlenet/desktopdata/cxmenu/Desktop.C^5E3A_users_crossover_Desktop/Battle.net.lnk" %u
2) Change/Create .desktop file to the appropriate shell file.
The other method is to edit the .desktop shortcut (or create a new one)
1) Open up in your favorite editor your .desktop file. You can create a new one too, by opening up Crossover, selecting the appropriate bottle, selecting BNet, and right clicking on it and picking "Run With Options", then clicking "Create Launcher". The new one will be on your desktop.
For me, my existing one is at:
2) Add in an EXTRA line, above the existing .lnk one. So for me I have
I did try the obvious just now of adding the preceding bit to the start of an existing .desktop file I had by just right clicking and it did not work, so if thats what you unsuccessfully tried, I hear ya. Too bad at least GNOME forces us into having to still go the extra mile to get some slightly advanced launch options for apps.