I'm using snow leopard.
In mail, command-delete deletes the whole line, option-delete deletes a word. As far as I can see, command-delete is not undoable - once the line is gone, it's gone. At least this is the case in Mail and Safari. Just tried it now - deleted the line then when I hit command-z to undo, all the text in the box was deleted. Had to choose redo typing from edit to save everything after the line delete. So there's definitely something funky here.
Final Draft can't be customized -- already talked with their system support.
Seems to me that if command-delete is consistent through mail, safari, ichat, etc, then it should be considered system wide. Any time one enters text, and one hits command-delete, there's a consistent effect of deleting the current line.
In the end, it's Final Draft's inconsistent use of shortcut keys that's the problem. These are the sorts of things you want to be consistent across apps and it's frustrating when vendors decide to go their own way, and not allow users the choice of being able to stick with what they know from other apps.