We solve a problem posed by Cardinali and Sastry [2] about factorization of $2$-covers of finite classical generalized quadrangles. To that end, we develop a general theory of cover factorization for generalized quadrangles, and in particular we study the isomorphism problem for such covers and associated geometries. As a byproduct, we obtain new results about semipartial geometries coming from $theta$-covers, and consider related problems.