Your 2013 Mac supports two modes of Windows 8.1/10 installation. In your specific case, if you upgraded from W7, the original installation was MBR/BIOS. Your Mac also defaults to a MBR/BOS installation of W8.1. DU warns you that Windows will not work, if you create an additional partition.
It is not a software bug. The issue in the thread and yours is a combination of BCD in EFI partition, MBR limitation of 4 entries, and manually creating an additional partition. This is unsupported under a BIOS/MBR installation due to limitations of MBRs (4 entries) and three partitions already in use - EFI, OSX and Recovery HD.
The other method of W8.1/10 installation is GPT/EFI which is supported on your Mac. I have it installed on a 2013 rMBP using this method. The BCD is no longer stored in the EFI partition. It requires creating a Free Space partition which is split into MSR/MSD parts. This method uses GPT-only disks, which allows you to create additional partitions using DU.
You must still install BC drivers for Apple hardware to work properly in Windows.