APG will never do as a good a job of RAW conversion than a more specialised tool.
I guess not, and I suppose that limits the usefulness of the detect in folder functionality (which I like, as I tend to take a mixture of panos and single shots in normal usage) in cases where the folder contains raw files, unless one does an initial temporary conversion of the whole folder to a subfolder using LR or any other specialised tool.
I am also curious about Autopano's performance with DNGs. Does it handle recent versions of the DNG standard better than older ones? I will do some experiments and report back.