In our particular sampradaya, we have books like Brhad Bhagavatamrta, Jaiva Dharma, and some others I'm aware of that are written in a story format. However, are these books fictional or non-fictional?
On the safe side I take them to be revelations by our acaryas, and the lessons you learn from them are invaluable, but unless it's specifically stated otherwise, I don't really know.
I don't mean that the philosophy is questionable, or if some of the other "spiritual" information is found in the standard scriptures or if they are revealed.
I'm just wondering if the characters involved in Jaiva Dharma (Sannyasa Thakura, Paramahamsa Babaji), Brhad Bhagavatamrta (Gopa Kumara) are actual living entities, or are they just there to act as characters to prove the point of the book or whatever.
Gaudiya Vaisnava literature is not to be analyzed as we are used to in the West. The point is not in whether the story is true or not. The point is what it wants to convey, ie what it wants to teach you.
Check the following for more details: http://www.uttama-bhakti.org/forum/viewtopic.php?f=28&t=68
As for how others quote sastra, I am afraid I can't say anything in that regard.
However, you seem to suggest that if the book is fiction, it cannot be quoted to prove a philosophical point. I, for one, don't see it as a problem. The story has simply been chosen to better convey certain point, and if it manages to do so, what does it matter if it is fiction or not?
Brihad Bhagavamritam has been written to convey certain philosophical points, and certain storyframe has been adopted for that purpose. Why should it matter whether all those characters really lived if the points are conveyed and the reader grasps them?