In this case you don't need the redstone engine and wooden pipe. The quarry already outputs items by it self into attached pipes.What I ended up doing was similar to what you suggest there Rhn. I got rid of the Itemduct, void chest, and Crystal chest at the Quarry side and hooked the wooden transfer pipe straight to the quarry hooked into the Phased pipe and I do like you said I send it all to the house and void the fodder there and do my sorting
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And yeah this is much easier, just have a Diamond pipe on the other side separating out all the items you don't want etc.
If you can avoid steps where you put items into inventories and then have to take them out again, then all the better.