Philosophy is a subject with very porous borders, and, as has been pointed out by others here, disciplinary distinctions don't always correspond to anything important. There are plenty of questions theologians discuss that philosophers also discuss, such as the problem of evil, which has been much discussed elsewhere on this site. There are, however, different ways one can approach such a question, and it's there that the difference, such as it is, between philosophy and theology lies. A theologian might draw upon certain religious traditions or certain religious texts in crafting an approach to the problem of evil. A philosopher would not do so, or at least would not treat those traditions and texts in the same way. One does not get to appeal to the "revealed truth" in philosophy—that's not how the game is played—any more than one does in physics. Of course, the same person might be both a theologian and a philosopher, and write about the problem of evil from each stance, even mixing the two perspectives in a single paper (or sentence!). So there are methodological differences between theology and philosophy.

There are also questions addressed in theology that are not terribly philosophical. In Christian theology, an example might be the questions addressed in Christology, which studies the question to what it amounts that Jesus was the Christ, that is, the Messiah. Obviously, this question only arises within a certain religious tradition, and one would suppose that appeals to (what purports to be) revealed truth would be in order there. In that sense, theology tends not to be neutral between different religious traditions. Although Christian and Muslim theologians can talk to one another and may study some of the same questions, some of their questions will be different, and what one regard as relevant to the study of one question the other might regard as utterly irrelevant. Philosophy, at least officially, tends to regard itself as neutral in such disputes.

As I said, there isn't always deep significance to distinctions between disciplines, but perhaps we can now see that there are some differences between theology and philosophy. And perhaps the reason for the sense that theology was "removed" from philosophy has as much to do with the emergence of religious tolerance in the eighteenth century and resulting changes in how philosophy was conceived. That's just a guess.

As for the last question, regarding medieval philosophy, it is still included because there is much philosophy in such texts, even if it is sometimes (or even often) intertwined with theology.