Basically, you can think of the Mistress ability flag working as, "If a skill has one gemstone requirement, nullify that requirement." I believe that before, it was explained that the "minus one gemstone requirement" flag was not able to stack for some reason, and therefore it only works as such.
So Basilica requires all three gemstones to work. Abracadabra needs both. Ganbantein needs both, I can confirm that point.