All the item pipes/hoppers that i've attempted to use keep pulling the egg from the scanner slot before the machine has a chance to scan it. Doesn't interact with comparators or redstone, and there are visually different ports on the sides for viable and non-viable eggs. I used Modern Industrialization pipes, vanilla hoppers, pretty pipes, mekanism pipes, even pulling upgrades from sophisticated storage, and not one will pull from the side slots and instead they go immediately for the input slot.

I've ran into this as well, unfortunately:( tried all the same things you did too