It seems that you wish to program only AT89C51 and thus have some confusion.

If you carefully look at the schematic, you can quickly realize that

1)Function of T5 is to switch the o/p of U7 at either 12.1V or 13.1V (using VPS signal)

2) This voltage (if required for a particular chip) is applied to the chip by turning on T3 with VPE signal.

3) If T3 is not turned on, the the pin 31 is automatically held at 5V using R7 and D2.

So if T3 is off, pin 31 is at 5V. If it is on, pin 31 is either at 12V or 13V approx. depending upon the status of T5.

These different Vpp levels might be the requirement of other derivatives. So don't worry and go ahead.