This is intentional, because they are options that depend on the engine. Only engines that report scores in a non-standard way need them (there aren't many of those, but Crafty is an example). For such engines you would include the option on the install line manually (by editing the engine list, e.g. through the menu item provided for it).
These options are only provided for erasing differences between engines that report scores in an opposite way. Storing them in the settings file would apply them to all engines equally, completely defeating the purpose of having such options in the first place.