For glass I'm mostly using the TiC smeltery now, outside of glass used in recipes. But yea, at full speed it takes about a stack and a half of ore to start using the 3rd processing slot at full speed going from purification chamber > crusher (a single pulverizer is too slow, but an overclocked macerator might work) > enrichment factory. So yea, the factories are more for processing multiple ores of different types, rather than a lot of a single type. That said, BC pipes are too slow to pull the dusts out of the machines quickly enough with max speed upgrades, so you're gonna either be using routers or AE to do it.
Just did a bit of testing, you can set up a purifier, crusher, enricher, and smelter (last three are factories) with 3 routers in a 2x2x3 shape around a single wire and the routers will know which factories get which part of the process, so the clumps always go to the crusher, the dirty iron always goes to the enrichment chamber, and the iron dust will always go to the smelter. Sadly it will force them into one slot at a time unless you're processing multiple ore types and it will take some machine filters and ejectors as well as dark iron, but it's faster at transfering items than buildcraft pipes and will probably be more space efficient than an AE setup.