There was some inconsistency in parse_args where some settings were set directly and others were adding to changed_settings and thus deferred.

This change simplifies things by simply directly setting in all cases.

The two differences between direct and deferred setting are:

• Direct settings are always overwritten by explicitly -s settings, even when the -s setting comes first, because explcit -s flags are all processed later.
• Direct settings don't end up in the user_settings map.

I don't think either of these differences matter for the settings in question here.