The Shared with Me area in OneDrive is a representation of permissions.
Without Skipped Linked Files
When we copy linked files, we can assume that the shared folder on a user's OneDrive is the only copy of those documents that matter with regards to permissions. As such, when we copy this folder, even though we copy files owned by another user to that user's OneDrive when that user's OneDrive is copied as orphaned files in the 'Shared with Me' folder in the Documents area, we do not copy permissions on these files. This has the effect of generally having one set of files that have permissions which should (generally) be mostly complete. This will have the effect of making the 'Shared with Me' area neater by comparison to the below, at the expense of this method creating duplicate files with the files shared from a user's OneDrive, and making them all owned by that person rather than the original user.
With Skipped Linked Files
If you have three other users who share a folder with you, there will be three folders in your 'Shared with Me area in OneDrive.
For example, this account in Google Drive
Would look like this in the Shared with Me area in OneDrive.
In migration, each owner of the file in the 'EXAMPLEFOLDER' will create a folder to contain that file with permissions to each user who originally had access to it. Since each folder with permissions creates its own entry into the Shared with Me area of OneDrive, you will end up with multiple folders. In addition, the users files end up in the folder called, Shared with Me in that user's Documents area.
What is in each of these areas?
In the EXAMPLEFOLDER shared from the Chris OneDrive account, there is the file that the chris account owns.
In the EXAMPLEFOLDER shared from the google OneDrive account, there is the file that the Google account owns.
In the EXAMPLEFOLDER shared from the Scott OneDrive account, there is the file that the Scott account owns.
In the folder in the Shared with Me in Matts Document area, are all of the files that Matts account owns.
Why are the documents copying this way?
Because Google Drive operates like Linux/Unix in that it uses links to refer to files. So you can have a file in as many places as you like at the same time. It can simultaneously be in many user's "Shared with Me" area at the same time as it's in one or more user's Google My Drive. If a user edits any of these files, they are editing each of the files. Each of these users has a perfectly valid claim to be able to use this file.
There is no equivalent functionality in OneDrive, since it lives in the windows world.
Another important reason to copy these documents is below. Look at the google Google Drive.
There are files here that nobody else should see. If these files were copied to a different drive, their permissions would be incorrect, since a user can always see all the files on his or her OneDrive, since they are a Site Collection Administrator for their own OneDrive.
Look at the same folder with SCA.
As you can see with SCA, these files copied over. But when you look at Matt's view, he does not see these files, which is the correct outcome.