[pakrat2k2]

IF I remember correctly the earliest version was in location as you specified, C:\Program Files (x86)\Eidos Montreal\Thief\Binaries\Win64/32
but after updating game to latest version the EXE's ARE in C:\Program Files (x86)\Eidos Montreal\Thief\Binaries2\Win64/32 .... the location DID change to new location.
so Update your game to latest version or

try this then..

Just create a Setup.ini file with your [Executables/Shortcuts] values and Save the ini file in the same folder as the Setup.exe.
This additional ini will 'override' the settings in Setup.exe

[Executable1]
Name=Thief X64
Exe=Shipping-ThiefGame.exe
ExePath=Binaries\Win64
Icon=Setup.ico

[Executable2]
Name=Thief X86
Exe=Shipping-ThiefGame.exe
ExePath=Binaries\Win32
Icon=Setup.ico

See if this then allows the shortcuts on desktop to be in correct folder location.
IF it doesn't work then use different conversion or wait till peter comes back & fixes it.