I have a similar issue. Since the auto web-deployment regularly fails, I would like to have the manual install put the correct 'profile.xml' file placed into the cisco profile folder, automatically.
I have had this work locally using msiexec /i <anyconnect-installer-name.msi> transforms "transform-name.mst" (the xml file also has to be in the same folder). When I upload the transform to the ASA, and attempt the manual install - it appears to be ignored (file size is also identical to the original .exe)
I've covered most of the limited documentation available on this but i'm still unable to do get it working.
As a side note, I used Insted it! to create my transforms as orca has a common issue of destroying MSIs when you create a transform for it.