Fruit flies breed new generations every oher day; that was the entire point. Those experiments involved more generations of fruit flies than there have ever been of humans or “proto-humans” on this planet.
Yes, but they were not exposed to countless millenia of environmental exposures that could have influenced them. For example, once upon a time, some insect might have landed on fresh tar oozing from the ground, thus becoming exposed to polyaromatic hydrocarbons that could be mutagenic. I doubt that happened in the lab.
Remember, even buying 1,000,000 losing lottery tickets wouldn't mean there's no likely winner in a lottery that's SO huge. Nature has drawn countless zillions of times.