PDF added to iBooks on Mac does not sync to iCloud Drive or my iPhone
Well, it turns out the answer was rather simple. I had iCloud enabled on my Mac, but it was not specifically enabled for iBooks. (Perhaps it was initially disabled because it is a new feature in recent versions of Mac OS).

I went to System Preferences -> iCloud -> iCloud Drive (click on Options...) -> click the check box next to iBooks to enable it.

After doing this, I immediately saw my PDF in iBooks on my iPhone (the one that I had added to iBooks on my Mac). I did not see the PDF within the iCloud Drive folder on iCloud.com, but I guess I can treat that as a separate issue since at least I've confirmed the sync worked.