There are many other primate characters that have been found in megabats. Thiele et al placed Rousettus in the frame with the long axis of the skull horizontal, an orientation that places the visual axis looking up at a large angle. In flying foxes the normal orientation of the snout during flight is tipped downwards at 40-50 deg. This orientation during mapping may have resulted in an exploration of the far inferior field where the decussation is both hard to define and misleadingly shifted. Rousettus may be genuinely different, having lost some of its visual specialisations perhaps as a result of its cavernicolous habits.
Most megabats roost in the open.
Whichever view one adopts on the question of Rousettus' apparent lack of a primate-like midbrain, it seems premature to dismiss a hypothesis that has generated so much interest and new studies. Given the intense interest in the flying primate hypothesis, and its clear stimulating effect on the generation of new studies, it seems premature to cast the hypothesis aside based on evidence from methodologies that are themselves in tumult. It is curious how passionate scientists become over phylogeny, especially when one considers that phylogenetic hypotheses can never be verified in the usual experimental ways. Linnaeus obviously thought that there was something in it, perhaps because he examined a flying fox rather than a microbat before he put bats in his Order Primates. I think that the social scientific aspects of the flying primate debate would make a wonderful PhD topic for someone interested in the sociology of science, irrespective of the rights and wrongs of the proponents on each side.