Assuming that power requirements can be met (through an external PS if necessary), is it possible to connect two hard drives to the IDE header of a RB230? For instance, CF → Primary, IDE0 → Secondary Master, IDE1 → Secondary Slave? Does the interface support such a thing?
if its a standard IDE port… i don’t see why not? up to 2 devices per interface.. I’ve never seen anyone do it, give it a shot?
Never tried (and never saw a cable for) connecting two HDDs to that header, but I am full of hopes that it should work as it is just a standard ATA/IDE interface. Another issue you have unconsciously risen is secondary ATA controller existence which is absent on RB200 (well, maybe the controller does exist… I am too lazy to check the Geode docs… but the appropriate wiring does not exist for sure). In other words, CF and ATA drives are connected to the same controller. That is also why there is a jumper to choose whether the CF would be ATA Master or Slave device
http://www.unitechelectronics.com/idecables.htm has plenty of interesting 44-pin IDE setups, but it sounds like the CF and 44-pin header are both on the Primary controller, which means that unless I could somehow disable the CF slot, there would be no way to add a 2nd IDE device.
New question: Is there a way to disable the CF slot? Even if I did, is the IDE header hardwired (like cable select) by JP2?
It is not so much tragic 
If you do not use CF, I am almost sure you can use two HDDs. No need to disable CF. There is no such thing as additional CF controller, just the same wires going to both connectors (with a little additional stuff on CF conector).
At least that is how I personally understand it…