That's not fully true. Generally speaking all the non profit theatre companies on Broadway have shows that play limited runs during the course of a season. When South Pacific came, it was the second and final production for Lincoln Center Theatre. However, due to the fact that there was nothing scheduled after it, they kept it open all this time.
I know that this is not the case but I am about to give a hypothetical example. Let's say that Roundabout Theatre Company had another show scheduled for The Henry Miller's Theatre after Bye Bye Birdie. But, Birdie got great reviews and is selling well. They could choose to do one of two things. The first one is that they can close Birdie when they said originally would. Or they could keep it open for a little longer and push back the starting time of the next show lined up for that theatre.
Non Profit shows don't always make the jump to an open ended run. Yes, it does happen. But, it isn't that common. Hell, 39 Steps opened on Broadway at Roundabout and while it did get a transfer with a commercial producer, that is something that is rare. Same thing for Doubt. That play opened up with a non profit and then went to an open ended run.
Granted, the examples I listed were ones that were exceptions to the rule that most non profit shows don't transfer. This is due to the fact that it is just too expensive to do so.
I believe that LCT is keeping South Pacific open as long as it has because it is still making them money, it is still holding up well enough for an audience. And, it now has the record of being the longest running show LCT has done.
I think that LCT, if they are smart, would wait until the momentum for this show dies down before they bring in something else.
Keep in mind, that they are doing a good job of using other Broadway theatres and renting them out for their other shows that they wish to produce. Keep in mind that In The Next Room, Or The Vibrator Play was produced by Lincoln Center Theatre and that was done in the Lyceum Theatre. Joe Turner's Come And Gone was also produced by LCT but due to South Pacific being in their main theatre, they rented out The Belasco.
"If you try to shag my husband while I am still alive, I will shove the art of motorcycle maintenance up your rancid little Cu**. That's a good dear"
Tom Stoppard's Rock N Roll