Starting from your first question. Yes, I tried that and the artifact doesn't go away. Second, I don't use InDesign. I imported in after effects and the preview is raster based and looks the same as the png export. Also, I don't see the artifacting in adobe illustrator preview. Lastly, I was trying to use clipping masks as a way to avoid this problem but the same issue still persists with that method. I normally use transparent gradient shapes that are perfectly aligned and have the same outline as the base shape it's layered over. This is how I like to do my shading, but I am running into this issue. Am I not able to shade my artwork in this way? Here's a little GIF to demonstrate my method:
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