#2 is that your followers are much more likely to read a thread, since a thread of length N will appear in your timeline at least N times. I often scroll through my feed and see a (28/30) marker, view the thread and read the rest of it. (Yes, 30 whole tweets!) If you tweeted out a link to an article you wrote 30 times, nobody would follow you. Some people will tweet twice for people in other timezones, but that's all you can get away with for out-of-band links.
#3 is that a thread often evolves out of discussion that's already on Twitter, and must participate where that discussion is happening at the time. Reacting to fast-paced news is a key one. Take this example: Josh Chafetz (the constitutional law professor, not the Congressman) watches Twitter respond to the Arpaio pardoning, and tweets a thread on why people are hot-taking it wrong[^1]. The next day, he turns it into an op-ed[^2]. But what good is an op-ed about rushed hot-takes a day late?
Edit: I wouldn't be surprised if Twitter made thread counters a first-class feature. People use the platform how they want, and it will stretch to do what is needed.
#2 and #3, fair enough, though both of them sound like anti-features (spam, and fast soundbites over longer explanations) to me.