or the external drive is taking so long to spin up that the boot code is giving up and settling for the next best option.
I suspect that may be the situation. It is an external USB 3, but the port is USB 2, at 5400 rpm. Small and quiet, though.
Fortunately there should not be too much need to restart, and if the internal drive eventually dies (recall the SMART alert), then the external will be the only choice.