Why does Windows Search "Indexing Options" select the wrong drive if it's cloned?

First of all I can reproduce your problem:

The problem is caused by the system file \System Volume Information\IndexerVolumeGuid in each of the cloned volumes. Apparently you are right about the fact that the system is confused by the GUID(s) you see in those the registry entries under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows Search\CrawlScopeManager\Windows\SystemIndex\*, and this file should be the provider of the GUID(s).

Since the volumes are cloned, this particular file is identical among each of them just like other files. And it will NOT get "updated" (i.e. regenerated to avoid conflicts) when the volumes are mounted, just like the volume serial:

However, apparently this file is safe to be deleted, and once the volume is mounted again, a new one will be generated; the problem will be gone once ALL the volumes that owned a duplicated GUID are remounted with unique GUIDs (so a reboot may be necessary if it involves the current system volume):

Unfortunately, I am not sure if there's a convenient/safe way to delete it under Windows: