The question is not why weren't loyal areas included in the Confiscation Acts and EP, but how COULD they be included.

To give a rough analogy, police officers may confiscate the guns from a house of a dangerous suspect. That does NOT give them the right to confiscate the guns from all of the neighboring houses---of law abiding citizens---as well.

It did not matter how morally reprehensible slavery was, the institution was protected by law. It was only forcibly disrupted in those areas in rebellion and at war against the federal government.