If you automate them you can do other stuff while they're cooking.Here's how I view this kinda stuff - naturally, we want to automate everything. However, sometimes it's simply more trouble than it is worth. Charged Certus Quartz, for instance... I just sit there with a stack of Certus and put them into the Charger one by one, and I wait until I have 64 Charged Certus. Then I go make my Fluix Crystals by hand. I can pretty much guarantee I will be done long before the OP has figured out how to automate the Charger. That's not a knock on anybody, like I say, we all have the goal to automate everything in this game - but my point is, sometimes it just isn't worth it and I just take the time and do it manually. I dunno about you, but once I've got a couple of stacks of Fluix Dust, I really don't use the Charger after that point, I really have no need for 50 stacks of Charged Certus or Fluix.
I'm not sure how expansive of an AE system you usually build, but it gets tedious after a while when you make your system larger.