The first phylosophical article in which the meaning of topos theory for modern physics is discussed was written by I.A.Akchurin. It was published as supplement  in book H.Reichenbach "Phylosophy of space and time" (Moscow: Mir publ., 1985) and  called   Methodologocal analysis of the Reichenbach conception of spase and time"

One of the last phylosophical article in which the application of topos theory to modern issues of physics, especially to quantum theory, is discussed you can download below.
Rainer E. Zimmermann Loops and Knots as Topoi of Substance. Spinoza Revisited-- Preprint gr-qc/0004077