Thanks for your post. I got stuck on this too and it was good to see I wasn't the only one. Your post actually taught me about the prefs.txt file which I believe is the key to achieving what we want.
Try this:
Launch VMware Horizon Client stock standard, no command line options.
Log onto your server
Go to the settings cog and make whatever changes you'd like to appear as default such as desktopLayout, sharing locations, protocol
Don't launch any apps. Close VMware Horizon Client
The file %appdata%\VMware\VMware Horizon View Client\prefs.txt contains all those settings you just chose.
You can then create the folder structure
C:\Users\Default\AppData\Roaming\VMware\VMware Horizon View Client
and then copy the prefs.txt file there.
Any new user on that computer will adopt those same prefs.
You'd also need to push this out to existing profiles on computers.
By the way I also use the group policy template to set the Server URL and the Certificate verification mode
Ben Jongsma