Anti-endomysial and anti-tissue glutaminase antibodies are pathognomonic for Celiac disease, a hypersensitivity to the gliadin antigen of wheat. It mainly manifests in the jejunum and ileum. In adults, it presents as chronic steatorrhea and bloating, while in children it does the same but also causes failure to thrive. Histologically, it is identified by crypt hyperplasia and villous flattening. If you damage your villi, you can't absorb fat through the lacteals of the small intestine --> malabsorption.
PAS-positive granules in macrophages in lamina propria = Whipple disease, an infection with Tropheryma whipplei, an intracellular gram-positive organism. This would similarly cause a malabsorptive state but is not associated with particular antibodies, and might also manifest as arthralgias, cardiac, and neurologic symptoms.