Well, the runner was in motion past 3B. I don’t know for sure, but I suspect the run counts? Or maybe because the batter only received one base, the baserunner(s) also receive only one base?
I struggle with the lyrics as well. My daughters are in musicals. I’ll go to each showing, usually 3 or 4 per production. I get some of it the first time, more of it the next time, so on and so forth.