There are big differences between natural genetic modification done by organisms themselves and the artificial genetic modification done by ‘genetic engineers’ in the lab.
Natural genetic modification is precise and predictable. It happens in the right place, at the right time without damaging the genome, and as appropriate to the organisms as a whole in relation to its environment.
In contrast, artificial genetic modification is crude, imprecise, unpredictable and uncontrollable.
The artificially created GM constructs have to be smuggled in by (disarmed) pathogenic bacteria and viruses that infect the cells, or otherwise forced into the cells by gene guns or electric shocks. The artificial constructs get scrambled in the process and could land anywhere in the genome, scrambling and damaging the genome in the process. Aggressive promoters are used essentially to force foreign genes to be expressed out of context.