Repairing permissions on an external drive does absolutely nothing. I love it how a person without any technical insight calls Apple - who has designed the system in the first place — "stupid".
As a lifelong user and a tech manager for a small business, I'm not sure I'd call Apple stupid, but I WOULD call them *******s at this point. They created AppleRAID and pushed all mac users to gravitate towards it, and now they pulled the plug on it--yes, there is support through terminal, but it's incredibly counterintuitive since they refused to use any kind of standard, like mdadm, so even finding information on how to, say, diagnose and rebuild a R0 array inside a R10 is nearly impossible (especially with every search engine hungry blog using RAID as a keyword for El Capitan). It's not impossible, but the point is this: Apple's one saving grace throughout the years was its user friendliness, that most things could be done relatively simply. Not only did they remove a feature that MANY users were utilizing, they did so without any warning and without offering any solution, other than one you'd have to pay for. This isn't an isolated case, but it's the first one that really effects functionality. Ease of use is why I bought a mini and server to replace our Linux box in the first place. That was a $1100 lesson that paid off for less than two years; since El Capitan I've had a server that crashes for no reason and RAIDs that basically need full overhauls but without a working system to keep them mounted long enough to actually back them up to fix them, and NO SUPPORT for the underlying architecture of the drive structure. AND they make upgrades a pain in the ass if you revert, like I did, back to Yosemite, in that finding builds of any third party software that you need requires searching outside the store they built for you to use. Basically El Capitan implodes a number of aspects of their streamline business model at this point.
Basically Apple released an OS that was potentially destructive to longtime core users, and their response to complaints and concerns seems to be "**** em, they still buy iphones".
EDIT TO ADD: OH! AND they crippled basic functionality in the current DU GUI with poor programming. Don't believe me? Boot into single user and run fsck. On ALL my machines this fixed zeroing problems and improved performance. DU didn't pick up the problem in either the main partition or running from Recovery mode.