>>42560850>>42560876She did summon it.
In the game Rayquaza was too weakened and needed help reaching its power via the stone the player had that Zinnia told the player to keep.
In the Manga she reached Rayquaza but lacked enough of the stones to control it, as she rushed her plans, and Rayquaza went berserk and nearly killed her. Afterward Steven's father apologised for getting her Master, Aster, killed and putting them in that situation when he had experimented on Rayquaza. Zinnia didn't forgive him, as he was arrogant and not genuine, but she did forgive Steven, who had no idea, and entrusted the future to Ruby and Sapphire.