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Well, the Safety Clone is always going to have a lot of files opened on the original drive, because those items are shared. So that's normal.
But, the "Full Clone" is likely doing this because it's not named the same as the original "Macintosh HD" -- try that, Smart Update it, and I think it'll be resolved. Disk Utility/Disk Warrior aren't causing the problems as such -- these other items that have auto-started on you are... and those are starting from the original drive, due to the naming & aliases (these are internally stored aliases, not ones you create yourself). I can't explain the eDrive because I don't know how exactly they do what they do... sorry.
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