The garden may be Rappaccini's world in the sense that it's the thing that matters the most to him but it's also Rappaccini's world in that he controls what happens in it.

Rappaccini loves his garden. Giovanni looks down at it every day and envies its beauty and loveliness. He also loves the glimpses he catches of Rappaccini's daughter—the only person who touches the gorgeous flowers without personal protective equipment. It's clear that the garden matters a great deal to Rappaccini. He is obsessed with it and finds it more important than everything else in the world. Dr. Baglioni tells Giovanni this and also warns him to stay away from Rappaccini.

Rappaccini controls everything that happens in his garden. He has literally made his daughter poisonous so that she can tend the plants without protection. It's dangerous for anyone else to be in there. He has created new species of plants; the garden is quite literally Rappaccini's world. He has created it, molded it, and populated it with both plants and his daughter. Nothing gets out of it without his permission—which is why the antidote kills Beatrice instead of freeing her from her oppressive father and his garden.