I'm not sure why you say that. I have three identical systems, the sole difference is the disk, using one install (2 are clones), so each uses the same digital licence. I have used only one at a time for the past two generations of Windows with no ill effects.
I have three different disks in this machine, two are backup clones of the C drive so the clones are bootable. I operate from any one (at a time) easily. Surely you are not suggesting one would need separate licences for back up purposes ?