I've just submitted the following via email to Apple. No doubt we'll have a solution by the end of next week.
"Does Apple monitor the Apple support forums? I guess not. Are you aware of the pervasive problem that has existed throughout Mavericks and Yosemite with the external "disk not ejected properly" notification appearing randomly when the MacBook Pro (and maybe others, as well) is a sleep, or just the screen saver is on, or even when working actively with the computer? For me this has happened only with USB drives, not Thunderbolt drives, but with Western Digital, LaCie, and also an original Apple SSD in a USB 3.0 box.
No one has been able to find the offending file or files or operations associated with this issue, only that it seems to have started with Mavericks, and was not present in Snow Leopard.
Do you, Apple, think maybe an engineer or two could be spared to work on this?"