iCloud & iCloud Photos · Storage Studio and iCloud
Does Storage Studio find a file that's copied both in iCloud Drive and in my Downloads?
Short answer: Not as one set. The Duplicates window checks each source on its own — This Mac, iCloud Drive and each cloud account — so a copy in Downloads and another in iCloud Drive aren't grouped together.
Not as one set. The Duplicates window checks each place on its own — This Mac, iCloud Drive, and each connected cloud account — so its results describe duplicates within that source. A file with one copy in Downloads and another in iCloud Drive isn't grouped together.
That keeps each check focused and means removing extras in one place never touches another. To spot copies split across places, look at each source's results, or search in Finder for the file name and compare.
Within iCloud Drive itself, only files already downloaded to your Mac are compared. See duplicates in iCloud Drive.