macOS Sierra boot problem related to Apple SD Card reader driver
I had the exact same issue. 2015 MacBook Pro 13", AppleCare. 

It took three attempts for the Apple service agent to resolve the issue, over the space of one month. 

The first time, they replaced the main logic board. 

The second time, they replaced the whole top case, including trackpad and battery. 

It was only after I found this post and brought it to their attention (including the fact that the SD card reader was showing as a fault when I ran system diagnostics) that on the third attempt they replaced the I/O board which contains the SD card reader and thankfully it worked.