The Mutator sheet offers fine grain control over which masters contribute to an instance glyph. By selecting a glyph all masters for that glyph will be shown in the glyph line. Double click on the M column
for the master selection popover.
Removing glyphs from an instance
By unchecking “Include [name] in instances” this glyph will be removed from instance UFOs. For instance if you have glyphs that are part of a rule, but you don’t need them in the output.