Hello,
Please NTFS has the limitation, not Windows. Windows has got around the limitation by using GUID Partition Tables. In computer hardware, GUID Partition Table (GPT) is a standard for the layout of the partition table on a physical hard disk. It is a part of the Extensible Firmware Interface (EFI) standard proposed by Intel as a replacement for the PC BIOS, one of the few remaining parts of the original IBM PC. EFI uses GPT whereas BIOS uses a Master Boot Record (MBR).
If your motherboard doesn't support EFI, I suppose that you should not use GPT; otherwise Windows setup wizard could not recognize the HDD. For your current situation, I suggest you using dynamic disks or an application like unRAID or Windows Home Server that essentially aggregates your physical volumes by using dynamic volumes. I personally feel this is the least desirable and secure method.
Good Luck!
Andy