If the locking pin lined the pump up perfectly when it was installed at the factory I think the difference now might have to do with the timing chain stretch/wear on the timing gears.
If you locked the pump before your removed it and did not rotate the engine it should go back to where it was. But if it was a few degrees off before the pump was removed it should still be a few degrees of when you put it back on.
My thinking is that on an engine with wear on the Timing Gears/Chain that the IP timing pin will only get you in the ball park and you will still have to re-time the pump to get the exact timing.
On the vary last page (at the bottom) of that manual you posted after the IP Timing Pin is removed; #16 "Check start of deliveryh;set start of injection if necessary." Indicating that you should check the IP timing after the IP is installed and correct the timing if it is not correct.

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84 300D, 82 Volvo 244Gl Diesel