Looks like there is a bunch of Custom Actions that aren't getting run during the UI sequence for some reason:
MSI (c) (E8:B8) [16:57:10:832]: Doing action: CheckETACLTPrev
MSI (c) (E8:B8) [16:57:13:352]: Doing action: SetCA_APPSWDIR
MSI (c) (E8:B8) [16:57:13:914]: Doing action: SetECSDirScript
MSI (c) (E8:B8) [16:57:14:336]: Doing action: SetINGNetDir
MSI (c) (E8:B8) [16:57:14:667]: Doing action: FindCAI
MSI (c) (E8:B8) [16:57:15:159]: Doing action: FindINGNET
MSI (c) (E8:B8) [16:57:15:651]: Doing action: FindCAMCAFT
These actions aren't present in the TRansform Wizard log, although I'm not sure why. If they were skipped because of their condition, there would be an entry similar to:
Skipping Action: ActionName (Condition is false)
These custom actions look to be InstallScript, and if the entry point numbers are any indicator, this is a VERY complex setup, as these start getting numbered at 'f1':
MSI (c) (E8:0C) [16:57:10:892]: Invoking remote custom action. DLL: P:\TEMP\MSI2A1E.tmp, Entrypoint: f83
Difficult to say what exactly they are doing, but in a worst case scenario, you can see all the property changes that the custom actions are making in the log, and so you can account for this in a regular transform (although I realize this is very inconvenient).