Yes, cross breeding is genetic modification. When you breed, you mix genes from different varieties, sometimes even different species, and select the genetic combinations which are the most favorable. Breeding absolutely is modifying the genetics. True, it is different from genetic engineering, but you are still making modifications. This is why the term 'GMO' is a rather poor term.
Or, as in this case removing a gene to make something Monsanto can patent and profit more from while not really understanding (or perhaps they do but just don't care) the consequences of doing so.
Plenty of plant varieties are patented and sold for profit, genetically engineered and not. No one gets on Zaiger Genetic's case over pluerries, or UoM's case over Honeycrisp (the patent has since expired), or complains that Driscoll's breeds patented berries. If you don't like that, I don't see you offering to pay the salary of the people who keep the food supply afloat in a world with ever evolving pests, pathogens, and environmental stresses that you never consider because we do our jobs well enough that they never affect you.
Your accusation that genetic engineering is not well understood is just outright patently false. It is used as a valuable tool in basic research all the time, and on the applied side if anything, there's too much regulation on GE crops. It's gotten to the point where most publicly funded genetic engineering work never sees the light of day.