SharePoint Migration Tool v 2 Issue - Moving Folders After Migrating Issue

I can replicate this issue easily so this is definitely caused by the Migration Tool.  If I use the Drag and Drop way, the issue doesn't occur, but I need to migrate hundreds of Gb of data.

Create a folder called Project1 and input 3 subfolders called Subfolder1, Subfolder2, Subfolder 3.  Within Subfolder1 create Subsubfolder1, 2, 3, then repeat under Subfolders 2 and 3.  

Use the migration tool to copy Project 1 to SP.  This copies Subfolder1, Subfolder2 and Subfolder3 into the doc library, with all its subfolders and files.  Great.  

Now create Project1 folder into the root of the doc library and move the Subfolders into it.  This also works great.

Now we have Project2 with all the same subfolders as Project 1.  This is just the way it is and have 150 of these on our file server and cannot be renamed.

Use the migration tool on Project2 and it copies Subfolder1, Subfolder2, 3 and all its subfolders and files to the root.  Again, works great.  Now create Project2 into the root and move these folders into it.

What now happens is all the folders you previously moved into Project 1 are now gone and somehow get moved into Project 2.  Project 2 now has all the files of both.  You will still just see Subfolder1, Subfolder2 and Subfolder3, but all the subfolders and files from both are now all mixed in together.

Microsoft support says they don't support the tool and since the issue arise from the tool and not via drag and drop, it's not a SharePoint issue.

I migrated 5 of these type of project folders on the weekend for a total of 250Gb and now it's completely useless as no one can find anything.