I've got a pre-comp that needs collapse transformations to be turned on so I can use multiply as a layer mode. But when I apply Animation Composer's preset, it loses it's "Multiply" effect. What can I do?
This is a known issue. Unfortunately, we can't do anything about it :(
"When a closed mask (with mask mode other than None), a layer style, or an effect is applied to a nested composition with collapsed transformations, the layers in the nested composition are first rendered on their own, then masks and effects are applied, and then the result is composited into the main composition. This rendering order means that the blending modes of the nested layers are not applied to any underlying layers in the main composition, and that 3D layers above and below the collapsed layer cannot intersect or cast shadows on each other."
As our presets add sliders, and a slider is considered to be an effect - it will behave the way it behaves. So the only thing we can suggest is to use keyframes.