The only way, for now, to have the Boot Camp volume show up in Startup Disk with NTFS-3G installed and active is to have it mounted by Apple's integrated NTFS driver (while NTFS-3G can still mount other available NTFS volumes read-write, of course).
To do so, open a Terminal window and do this:
cd /Volumes/NameOfYourBootCampDrive
sudo pico .ntfs-readonly
... and then save the file with the usual ctrl-O, enter, ctrl-X; finally, unmount and remount (with Disk Utility) your Boot Camp partition.
This, BTW, will create a (invisible from OS X) .ntfs-readonly file at the root of your Boot Camp volume, thus telling NTFS-3G to bypass this volume and let it be mounted by Apple's read-only driver.
Of course, you will have read-only access to the Boot Camp volume, but it will still show up in Startup Disk.
Let's hope they'll eventually fix this in better ways (see full integration between NTFS-3G and Startup Disk)...