On the first point, they're just saying that 3 people seeing a doctor about flu symptoms at that time of year is not unusual (most Chinese routinely go to hospitals for any medical treatment), and that even if they did have Covid instead of flu they might have got it outside the lab. There were people in Wuhan with Covid back then, but there were a lot more people with flu. The odds that any given three people with flu symptoms in Wuhan at that time actually had covid was still very small.

On the route into humans, I'm no expert but as I understand it while these viruses are found in bats the most likely route to humans is via another mammal intermediate such as a pangolin or cat. The reasons for this seems to be that bats are just too small and the virus load too thin to pose a threat to humans. So bat to human is very unlikely, but bat to cat is more plausible, and then cat (etc) to human also more plausible. I've no way to validate if that's accurate.

It really is all numbers games though. All we can say is what is more or less likely, and I think that's all the article is trying to explain.