I have completed my upgrade to ElCap driect through Apple. But, as I said, the only way I could locate it at the AppStore was to look at software I purchased (thank you, Cory, for suggesting that). Now, I sure never shelled out any money for ElCap before, so I have no idea why the AppStore assumed that I "purchased it" nor why it had to be listed that way in order for me to get it. I have to assume that by making it REALLY HARD to install older operating systems, Apple is pushing people pretty hard to upgrade to the latest. Of course, as machines get older, they can't install the newest operating systems, so accessibility of the old ones gets more important.
Honestone, I assume your suggestion of ad/malware detectors was to check on the cleanliness of a third party copy. That's a good idea, and I use Malwarebytes anyway, but in principle, at an OS-level, people can do really nasty stuff that those detectors won't be sensitive to. If you own the OS, you can do ANYTHING. Interesting suggestion about saving the installation files, but if you get it from the AppStore, I don't think you get any such files. The AppStore just does all the installation work.