System Folder vs Users Folder: Why are Docs in System Folder?

JBHaber wrote:

Strange happenings on my Mac. I typed up a document in Pages, but couldn't find it my Docments folder.

If this is your only issue and iCloud Drive got turned on by default—I would look there for your Documents.

iCloud drive missing desktop and documents

Add your Desktop and Documents files to iCloud Drive - Apple ...

Set up iCloud Drive - Apple Support

How to Restore Your Desktop and Documents After Disabling ...

How to find your Documents and Desktop folder contents after ...

Finder>Go>Go to Folder>copy & paste:

~/iCloud Drive (Archive)

iCLoud Drive (Archive) - here you should find all your files 

JBHaber wrote:

When I migrated content from old Mac mini to my this new MacBook Pro M1, might I inadvertently restored the data to both locations?

Is this what you're looking for:

yes.

Something is different here then what I am used to seeing in a virgin install/upgrade. However I am not too familiar with the M1.

Also from your OP I am not clear where you got those screenshot of the complete file path (a little difficult to realize where theses came from, or how to interpret the complete path shown)

However for comparison a virgin install/upgrade to Big Sur (left) vs your Drive structure:

Where is your "Macintosh HD - Data" volume?

edit: I do see now you do have "Data" <5: APFS Volume ⁨Data⁩ 516.8 GB disk3s5>

About the read-only system volume in macOS Catalina - Apple ...

Another look is from the Disk Utility.app>View>Show All Devices

ex.

JBHaber wrote:

(I used Carbon Copy Cloner to manually restore folders)

But my new file appears in the System path, but not when I simply go to the Finder > Documents path.

hmm...

The most trouble free way to move to a new machine, is using the Setup Assistant on the initial boot— you have one shot here. https://support.apple.com/en-us/HT205749

If that opportunity has past, the second best way is use the Migration Assistant, a CCC can be a source drive.

How to move your content to a new Mac https://support.apple.com/en-us/HT204350

Lets see the output from the Terminal.app , copy and paste:

diskutil list internal

Not a duplicate or an alias. It's just file system magic.

The drive is divided into an OS drive and a Data drive.

The Data volume is mounted to /System/Volumes/Data, and the Finder makes it appear that the two Volumes appear as one.