The GUI object customization is best configured if you generate a startup script and then use the saved .vbs file to launch UFT and set the configurations. They persist while UFT is open and apply to newly recorded scripts. The existing scripts would use the properties saved with the test (or a shared object repository). This is important to understand as chaning the object indentificatin properties won't affect objects that have already been learned and added to the object repository. The settings would apply to new objects learned through recording or added manually after the configuration change.
Another benefit to launching UFT with a generated script is that the script can be copied to other machines and UFT can then be launched via the .vbs script and have the same object identification set automatically for those machines. Again, this would apply to new tests that are created. The object repository properties would be used for playback regardless of the settings since those were saved outside of UFT.