Bypassing NT port protection isn't problem, WinUAE does the same when accessing Catweasel using driver called WinIO. (of course administrator-level privileges are required to install the driver)
I think the biggest problem is interrupts/multitasking. Disk2FDI requires very exact timing to read the disk and background interrupts most likely cause timing problems. Writing special Disk2FDI driver is probably the only working solution.