You should probably add "+set com_hunkmegs 96" to the command line too. But why don't you just use a shortcut?

Anyway, when we release the standalone exe, it will probably start wq3 by default. So you can use it like you would with your file. The file is likely to still be named quake3.exe, for compatibility with external utilities. But you can rename the executable to whatever you want, so you can have one for each mod if you like.