%name-prefix overrides --name-prefix?

[Joel E. Denny]

In files.c, there's this comment:

/* Initializing some values below (such SPEC_NAME_PREFIX to `yy') is
   tempting, but don't do that: for the time being our handling of the
   %directive vs --option leaves precedence to the options by deciding
   that if a %directive sets a variable which is really set (i.e., not
   NULL), then the %directive is ignored.  As a result, %name-prefix,
   for instance, will not be honored.  */

Although that logic makes sense to me, Bison doesn't follow it.  Instead, 
for example, %name-prefix has precedence over --name-prefix.

Which way should Bison behave?