The Logistics System Entrace Pipe should have another mode were it will send all items that go through it to the destination pipe even when they already have a destination.

With that we could do this:
Chest -> Chassis Pipe with extractor module -> entrance pipe -> destination pipe

Right now this doesnt work and you have to look for another method to extract the items.

Ill look into doing that ;)
Should be as easy as switching the mode wwith a wrench hit.