Oh come on. This ending was the simplest and most classic of all story endings. What's there to be confused about? And no, no don't read too much into the -

"she didn't go back for the necklace. Does that mean she didn't want to be Queen after all? Does that mean Beatrix will be Queen? Maybe the necklace had dark spells brewing inside it that Garnet sensed because she's magic and maybe it's setting up for a villain in FFIX-2, yknow it's the villain that cursed the necklace."

NO. Jesus Christ, it was just a cheesy romantic moment.