That's really just a failure of imagination. Also, it ignores that the mechanisms of evolution have themselves evolved.
Sure, evolution seems unlikely if you assume discrete genes have to change in lockstep to adjust traits successfully (eg. if you assume that separate changes are needed to adjust bones, muscles, skin, nerves, etc. to lengthen a limb), but that isn't how our bodies wirk (if it was, it would be nearly impossible to heal from an injury), nor is it how genes control that development.
Instead, you have genes that control things in less direct ways, such as body to limb ratio, and other genes that direct development of things like muscles in relation to bones and joints don't have to change at the same time for everything to keep working.
Even that's an overly simplified model, but you should get the general idea. You might like to read the book "The Plausibility of Life", which goes into more detail.
> This study suggests that's not the only way these genetic changes happen
The study says nothing about the transfer mechanism, only that it took place.
From an evolutionary perspective, there are none. Both are but sources of variation (the actual cause does not matter) in the genome; which, depending on their impact, may or may not get fixated by natural selection.
But how the whitefly managed to swipe a plant gene is unclear. One possibility, says Turlings, is that a virus served as an intermediate, shuttling genetic material from a plant into the whitefly genome.