Here's an interesting thing about 16:9: When you get the computer to "capture in 16:9", all it does is add a little checkmark to the "Anamorphic" column to your clip in the Browser!
This should mean that, theoretically speaking, if you mistakenly capture a 16:9 clip without selecting the 16:9 capture preset, you should be able to go into the Browser and add the checkmark to "Anamorphic" to correct the problem.
I've never had to do the above, but I've also tried clicking on the Anamorphic checkmark in the Browser on a normal, non-16:9 clip. When I drag it into a normal timeline, it gets letterboxed and crunched. So I don't think there's anything native to the clips that FCP picks up on; it's all dependent on that little column in the Browser.