What I usually do to take up the least space and be the most efficient is have a macerator at least one block away from the ground, and a furnace diagonally down one block from it. This way you could just use buildcraft wooden pipes to pump into the furnace. Use a redstone engine to power it. You could use a transposer or filter to suck the items out of the furnace and use pneumatic tubes to get the ingot into your sorting system. I usually do this with every ore receivable. Using a transposer or filter to suck the items out of the macerator would be a waste for three reasons:
1. Space. It would take up to two blocks more per ore, which could be a pain.
2. Wooden pipes and redstone engines are cheaper.
3. Timers and sequencers could cause a hellish amount of lag.
Your right about "useing a transposer and filter would be a waste"but i want something fast and efficent, I dont really care about the space i need, I just have a crap ton of ore's collected that need to be processed