If I understand correctly, this is a limitation of x86_64 backwards compatibility rather than a limitation of Windows. Enough of the 16 bit behavior was preserved in 32 bit protected mode for Win16 apps to run, but nearly all of it doesn't work in 64 bit long mode (things like virtual 8086 mode aren't available in 64 bit mode). There's also all the GDT, LDT, TSS stuff on 32 bit x86 that was either dropped or reduced for x86_64.
Your only option at this point is to use a virtual machine. Intel has supported real mode VMs since Sandy Bridge and I'm not sure when AMD got it, but all of the Zen parts definitely support it.
