Genetic engineering is a technology not a trait.
In general, genetic engineering and genome editing are as safe as conventional breeding and mutagenesis (introducing thousands of random mutations by radiation or chemicals to speed up the breeding process).
The safety of the resulting product depends on what has been changed or how the crops are used. You can obtain unsafe products from conventional breeding, as shows the popular example of the Lenape potato (Wikipedia), which was bred for specific traits while unintentionally increasing its solanine content to dangerous levels.
The same goes for GMOs. Glyphosate resistant crops will increase the glyphosate level in the plant and favor unsustainable farming practices like large mono-cultures and a lack of crop rotation with potential risks for the environment or even human health. On the other hand, Bt-crops have been shown to reduce pesticide use and can therefore be beneficial for health and nature.
Your tomato example is not that much related to farming. The aim was to improve shelf life, which could help to reduce food waste. Similar products are non-browning apples (Arctic Apples). Usually, they work by blocking the activity of an enzyme that normally would degrade the fruit. 667
Of course, there are debates if the enzyme is needed for important processes in the plant and if it would have any negative effects on the healthiness of the product. But usually nothing significant is found.
Furthermore, genetic engineering can also make products healthier by introducing positive traits like increasing vitamin or healthier fatty acids.
Again, the safety of the product depends on specific changes and not on how these changes have been achieved. If we could have all these products with conventional breeding, we would do it. And we probably could, it just takes ages. So, all "negative impacts" of GMOs should really be discussed as "Do we want/need this trait and what are the effects?" and not as "Was it created by genetic engineering?".
Finally, GMOs are the best tested products on the market. While we know very well, what has been modified in these plants, we have no idea which genes have been changed in mutagenesis products. And because of strict regulations and research, approved products can generally be considered to be safe to consume. So far, there is no recorded case of someone having serious health issues from consuming GM-food, while people are dying from their self-grown zucchini (I'm not kidding). 667