Do not blame this upcoming response on me being lazy or playing too much Factorio, but I have to say this whole Inputs and Outputs only being in one specific Spot thing is related to the immense Lag it would cause if I went the Railcraft Route and just scanned every single Block around the Machine.
You can use Extenders to redirect Item Output one way, and then use a Pump Cover to have the Fluids go the other way though. Multiblock Machines are programmed to do parallel Processing at a somewhat uniform Rate so every Recipe takes roughly the same Time if possible. This also means you should have more than enough time to manually get rid of the Output by attaching a Hopper below the Machine or similar.
So yeah, this particular Issue is probably not going to be changed, as it would also mess up existing Setups.