so would it be accurate to say the “complex” blending operations from photoshop are not fully compatible with after effects? it certainly seems that way, considering one of the central uses of after effects — 3d layers — is essentially broken by implementing this feature. one cannot reliably expect layers from photoshop to properly depth sort or cast and receive shadows; nor can one expect the rest of one’s composition to do either thing properly. this is unacceptable, and has lead to hours of head-scratching and troubleshooting in high-stress production environments all around the world.
i suggest you either remove this “feature” or make it work properly. the current half-implemented form ruins one of the best, most used, and most important features of after effects.