Partitions can be marked protected via EFI. Windows sometimes creates some of these partitions during installation, and of course recovery/restore partitions almost always get marked as protected as well. Disk Management won't allow those volumes to be interacted with. GNU Partition Tool probably wouldn't care.
Within windows you can also use the command line equivalent to Disk Management, Diskpart, and use the "CLEAN" command (with the correct drive selected! For the love lf all things!) to completely wipe all partitions from a drive, including any protected partitions.