. . . the entire media file is exported"
The problem is cosmetic / workflow. This is how FCP itself handles media.
When you mark in/out points and drop a clip in the timeline, it's still connected to the whole file. This is obvious if you use the slip/slide tool, where you can then see the "outline" of the entire file in the timeline.
The problem people have is that although STP "highlights" the portion of the clip you're working with, you see the rest of the clip and it's easy to accidentally head off past the highlighted area. It MIGHT be better if you only saw the selected part of the clip you're working on with the OPTION to see the entire clip if you chose to affect it globally (sorta like removing the limits of a subclip in FCP).
One "solution" would be is to finish your FCP edit and then Media Manage the project. At that point your clip could/should stand as separate clips not connected to a long master clip.
Craig Seeman
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thirdplanetvideo.com]