I have an update on how to handle having a home folder at a location not on the boot drive. I had to make an additional changes to what I said above in order to get everything working. Based upon what my El Capitan has been doing, I have a hypothesis on what Apple did to cause this problem, and that could help with our various work-arounds.
In the current version of El Capitan (10.11.1), Apple hardwired the App Store to look for the folder "Shared" on the boot drive (at boot/users). If there is a symlink to another drive, the App Store will not recognize it. The AMD error occurs if "Shared" is not found.
Other Apple processes also look for the folder "Shared", but they expect it to be at the same location specified for the home folder in the Users and Groups System preference discussed in this thread. If there is a symlink for Shared at the specified location, the other Apple apps honor the symlink. Thus if the folder "Shared" is on the boot drive, and there is a symlink to it on the non-boot drive, the Apple apps will follow it.
So, for those of us who have relocated the home folder, whether via a symlink or via Users and Groups, here's what I believe may work until Apple fixes this.
1. The home folder can be relocated either by a symllink at boot/Users or via the Users and Groups preference.
2. The folder "Shared" must be located at boot/Users.
3. There needs to be a "Shared" symlink in the folder containing the home folder.
Note: If you wish the non-boot drive to be bootable, then it must as well have an actual folder "Shared" in addition to the symlink "Shared".
When I moved the folder "Shared" back to the boot drive, but before I performed step 3, my computer would crash about twice a day, presumably from Apple processes not able to find "Shared". Also, Spotlight didn't crash but all searches came empty. All is well since I performed step 3 although it has been only 1 day so there is still time for something else to go wrong.