You can use the MSIIs64Bitparameter to install 64-bit applications at ProgramFiles directory.
On 64 bit OS ThinApp installs MSI package application at ProgramFiles(x86) for 32 bit MSI package. For 64 bit MSI packages user should set MSIIs64Bit parameter in package.ini file to install application at ProgramFiles. This parameter will be present by default in Package.ini if application is captured using 5.0 build.
[BuildOptions] MSIIs64Bit=1
