This works for me. In my beautifier profile (Tools -> Beautify -> Edit Current Profile menu is one way to get there), under Spacing -> Expressions -> Function/Method Calls, I turn on "Pad inside parenthesis", and turn off "Space between empty parenthesis". Then when I type something like this:
foo(a,b);
...when I type the ';', the code gets changed to
foo( a, b );
At the very least, the context tagging setting you mentioned should probably not be a separate setting for languages that have beautifiers, but should be linked to the beautifier setting. Otherwise, it is confusing. Not as sure for the auto-close setting.