The installer from IBM, notes_designer_admin_851_w32_CZ5S0EN.exe, has 2 options on initial launch.
1. Install and cleanup the install files after setup completes.
2. Install and leave the files to be used again.
The second option corrupts the files. Instead I started the install and then copied the files out of the temp directory in my profile.
I used these instructions as a guide.
I created a Record MST for the changes below and added the standard CRA changes to. I saved it and created Data2.cab and LotusNotes851.mst.
I found properties that get created/populated when the transfom is created. They reference the installing users profile and they don't exist in the native MSI.
I've found that if they are deleted, the install.xml that is created at the time the transform is created is not referenced and prevents an error that it can't be found during install.
For ALLUSERS=1 to be 100% true if you want this install to be for multiple users or possibly for use when using a deployment tool (eg: install runs as System), ApplicationUsers needs to be set to AllUsers.
I changed the Setup.ini to add the following line.
CmdLine=TRANSFORMS=LotusNotes851.mst /liwear "%LOGFILEDIR%\%PACKAGE%_MSI.LOG" /qn