Fix "default" encoding to match "auto" encoding except for the actual output

Fix "default" encoding to match "auto" encoding except for the actual output
of \inputencoding commands, which are not needed in some cases (e.g., Hebrew
with ivritex).

This fixes some of the remaining problems (but not all) from bug 3613 (namely, http://bugzilla.lyx.org/show_bug.cgi?id=3613#c9).
See also some example files fixed by this in http://permalink.gmane.org/gmane.editors.lyx.devel/88805 .

git-svn-id: svn://svn.lyx.org/lyx/lyx-devel/trunk@18994 a592a061-630c-0410-9148-cb99ea01b6c8