Towards the bottom of the first amud it says, that if someone was sold by the Beis Din, maybe he should not go out at Yovel because the master will lose his remaining money(Rashi). However, this does not make sense, the master would not pay a full six years worth if there is only three or four... years left to Yovel?
This is an excellent question. The only source that I could find that asks your question is the contemporary work, Beis Lechem Yehudah, who does not offer an answer. I can only suggest (b'Dochak) that had the Torah not explicitly stated the Halachah that Machruhu Beis Din goes out at Yovel, then we would not have factored it into the price, and it is only now that the Torah wrote an extra Pasuk that we consider the sale valid until Yovel.
However, Rashi writes continuously the term "Paga Bo Yovel" which would allude that it was coincidental and not predestined.
The Rambam (Hilchos Avadim ch. 2) writes that if someone sells himself for ten or twenty years and Yovel comes even after one year he goes free. Even if we were to say that Beis Din's sale is a standard six years even if we know that Yovel is coming, surely when someone sells himself -- where he sets the terms -- the original sale should only be until Yovel.