Still a mystery, with no consistent indicator of cause.
I've gotten lucky; no issues since replacing my external 4-bay enclosure, via warranty.
But I'm not convinced it's NOT an Apple hardware/firmware issue. It's worth repeating that my eject incidents go back to a recently-acquired 2008 Snow Leopard iMac. And then reappeared on a new 2013 iMac, now on El Capitan. In both cases, the problem only happened with the 4-bay enclosure, and not with multiple free-standing HDDs. The problem showed up when connected via FW800, USB2, USB3. I don't have a Thunderbolt external. No USB hubs.
I bring this up to underscore the wide variety of scenarios in which the eject issue happens. It still strikes me as some kind of voltage mismatch between the ports. If it is hardware-related, I wonder if PC users ever experience such issues; if not, that fact might create some insight.
The very last thing I did before the problem appeared on my 2013 El Capitan iMac was update my iPod Touch to the latest iOS. I used my live AppleCare status to discuss this with a tech/rep who seemed very knowledgeable. He thought that MAYBE the iOS update included a routine update to the iMac port drivers, but that wasn't definitive. But it does suggest that there is a delicate voltage(?) balance that needs to be struck between workstation and externals.
From reading here, it appears that Apple has closed the door on this, using the tried and true we-can't-replicate-the-issue rationale. They should at least keep the door open, and if nothing else take it into account for the next major OS update.
Since I don't have issues right now, I'll try to keep it that way. I just won't update the iPod Touch any more; it's not critical.
But it sure diminishes confidence in the It-Just-Works motto.