Fix jank when dismissing InputMethodAndSubtypeEnabler.

InputMethodAndSubtypeUtil#saveInputMethodSubtypeList() has a bug that
it saves implicitly enabled subtypes when "Use system languages" is
checked.  Implicitly enabled subtypes are transient data and the system
should have only a null data (0) in the persistent strage.  The root
cause of this bug is that the method in question has not checked whether
the preference item is in enabled (not grayed-out).   If it is
grayed-out, its checked state does not mean that the user manually
checked that subtype but it is just an indicator for the user.

The strange UI jank when dismissing InputMethodAndSubtypeEnabler is one
of the victim of the above bug because we have worked around it by
actually changing checked state before calling the method in question.

With this CL we no longer need to update preference items in
InputMethodAndSubtypeEnabler#onPause().

Bug: 27867966
Change-Id: Ifc291d77ea41a988438765b9ba16bc5d18a15e1b