Under the extra-inning rules, each half inning beyond regulation is started with a runner on second base. The runner is either the ninth batter due to bat in the current inning, or a pinch-runner if the batting team so chooses.
I see this sentence in this article. "So choose" seems to be an idiom. I also found another example on this site:
I have two free concert tickets for tomorrow. We can see the concert at 7 pm and still be home in time to catch mom and dad before they leave. If you are not into it, just let me know and I can still sell the tickets in a split second. We can still watch the concert on TV if you so choose.
It has an explanation about the phrase:
'If you so choose" is used when a person is given an option of choosing between different things.
But with that limited explanation, I still can not get the phrase thoroughly. Can someone help to elaborate it based on the given examples above?