Interestingly, if I add them back it still uses gtk_buildable_set_name instead.

My workaround is adding the following extern declaration:

/* Workaround for https://bugzilla.gnome.org/show_bug.cgi?id=647122 */
extern void gtk_file_filter_set_name (Gtk.FileFilter filter, string name);

And replacing:
filter.set_name (name);

with:
gtk_file_filter_set_name (filter, name);

GIDL has no information about methods that are not an implementation of interface methods. Then the vapi writer just skips writing interface method implementations.
The solution would be to mark the method to be "new", then fix vapi writer, then gidl parser and finally the gtk3 metadata.

This is really a more deeper bug, it's whether vala should allow "new" keyword for method implementations or not.

commit 924b23bee3e67de575c20c70c7a89ddddb2b5c30
Author: Luca Bruno <lucabru@src.gnome.org>
Date:   Mon May 23 19:29:50 2011 +0200

    gtk+-3.0: Add FileFilter.set_filter_name and get_filter_name
    
    Vala does not allow specifying methods that do not override interface
    abstract methods (get_name and set_name in this case from Gtk.Buildable).
    Workaround the issue by renaming the methods as this feature isn't
    going to be implemented anytime soon.
    
    Fixes bug 647122.

This problem has been fixed in the development version. The fix will be available in the next major software release. Thank you for your bug report.