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

The issue of being able to pull from the input slot will be resolved with the next PolyLib update.
But it should still be possible to automate the Ovoscope even with that issue because the block will push the egg out either side of the block depending on its viability. So rather than pulling the item, you should be able to use a passive pipe, or worst case, place an output chest on either side and pull from those.

PolyLib 0.4.170 is now out and should resolve this issue