Or you can install the .exe on a test machine, take a copy of the folder Scratch Desktop from C:\Program Files (86)\ (I think could be C:\Program Files) and put it in a network share and create a GPO to create the folder structure and copy the files to the computers you want it on. Then create a shortcut that points to where you copied the files to that points to scratch desktop.exe, for me the path was C:\Program Files\Scratch Desktop\Scratch Desktop.exe.
My GPO:
Computer\Preferences\Windows Settings\Folders
New Folder: C:\Program Files\Scratch Desktop
New Folder: C:\Program Files\Scratch Desktop\locales
New Folder: C:\Program Files\Scratch Desktop\resources
New Folder: C:\Program Files\Scratch Desktop\swiftshader
Computer\Preferences\Windows Settings\Files
New Files:
Source \\Your\Network\share\Scratch Desktop\*.*
Destination C:\Program Files\Scratch Desktop\
New Files:
Source \\Your\Network\share\Scratch Desktop\locales\*.*
Destination C:\Program Files\Scratch Desktop\locales\
New Files:
Source \\Your\Network\share\Scratch Desktop\resources\*.*
Destination C:\Program Files\Scratch Desktop\resources\
New Files:
Source \\Your\Network\share\Scratch Desktop\swiftshader\*.*
destination C:\Program Files\Scratch Desktop\swiftshader\
Not as clean as an msi but if you want to do it all via gpo thats the workaround I came up with.
Note: Make sure the folder "Scratch Desktop" you copy to the network share has read access for authenticated users or the files wont copy.