I don’t think it is autonomous rationalism to begin one’s apologetics with theological proofs. The whole point of beginning with reason is not to start from a neutral ground where all facts are brute facts and everyone agrees that religion is not an issue. The point of beginning with reason is to demonstrate the necessity of faith. One must differentiate, as St. Anselm did, between an “independent” argument and an argument made directly from Holy Scripture. Neither can be called “autonomous.” Both presuppose the necessity of the Triune God.
Autonomy
Published
EPISTOLÊ 
BTW: Those who say that reason is not an accurate tool for the demonstration of the faith ipso facto open the door to skepticism. Our knowledge of reality depends on the authority of God that he adequately reveals himself through creation (implying that creation can be known). If we cannot use creation as a method in apologetics then it is difficult to defend our own epistemology based on the doctrine of creation.
Since you enjoy the Scholastics, have you checked out Henry of Ghent on this exact issue (the accuracy of reason)?
Tim,
No, but I’d love to. Is this in his Summa?
Eric