I hear what you're saying... and I have also run my En-El15s down pretty good... Nikon has been putting Lithium batteries in their cameras for a long time... and I'm not sure if the concept of a switch to limit whether the cells drop below the threshold shuts if OFF to prevent complete draining was in their original specifications, and at what point they may have slip-streamed the feature in their batteries...
If the battery has a meter that can be spoofed by constant charging, and the meter becomes inaccurate, I don't know how the battery in that condition can accurately determine when to turn the battery OFF to keep from draining beyond its recovery threshold...
As a safety precaution, when on a shoot, I always carry at least two extra batteries to keep from getting too low...