The reason is quite clear: because otherwise one could very trivially escape the GPL's requirements entirely, by making some little modification directly to the binary for some program, and then claiming that the binary is, ipso facto, the preferred form.
No, because a reasonable person (or, more accurately, a court applying that standard) would not find that to be the preferred form of modification. In the very least, he'd have to rise to the standard of creating a derivative work.
OTOH, a if he made substantial changes, it would be.