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AFAIK, this is by design. Under settings - users you can only select to include hidden items. Guess that one shoud work, independent from the place of your home dir.
It's a "rollback" for your system files.
For "user data" you can use backintime (or any other convenient program of course).
My user files are also at a different disk and I use backintime in combination with timeshift.
Both have never let me down thus far (I cross my fingers).
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