All I can tell you is that it has always worked for me, but you can always put in a clean hard drive, and install Windows on it with no other drives plugged in and know for sure where the boot sector will be.
That's what I did when I updated from Windows 8.1 to Windows 10, I put in a new SSD unplugged the other drives and then installed Windows 10 on it. When I plugged the other drives back in it still booted to the new drive no problems, only then did I remove my Windows 8 installation from the old drive.
Things like this are a good reason to have a system image file, no matter what you screw up you can get everything back the was it was in a reasonable short period of time.
I use a free program called EaseUS Todo backup and recovery, it's free, and it's always worked for me. It has saved my from hours of messing around many times.