Short answer, no, Fantastica guests aren't being upgraded to Anytime dining if they're being seated with their Aurea friends in Green Wave. It's simply the largest dining area with the most seating.
The Green Wave (deck 5), Jondal (deck 6), and Agean (deck 7) are all for Bella and Fantastica guests. Of those three, which dining room you get is based on which assigned dining time you have. Aurea guests are seated via any time dining at Skyline (also on deck 7). All four of these have the same menu and, therefore, probably the same kitchen. If there was extra seating at one of the assigned dining times, it looks like they were able to accommodate an Aurea guest or two who would otherwise be seated in a different room ordering the same stuff.