Modifications happen naturally too it just takes a long time. Domesticated crops have been genetically altered compared to the wild plants that they have been from.
By grafting different plants together, people have been creating transgenic plants (plants that contain genetic material from an unrelated organism) for a millennium.
Additionally, research has found naturally occurring transgenic plants; some of these plants (such as bananas and peanuts) contain the exact same bacterium (Agrobacterium microbe) that scientists typically use to create GMOs.
If these modifications can happen without human intervention, then they cannot be claimed to be unnatural. Modifying organisms in a lab is just speeding up the process. It is the next step in agriculture.