I don't think I would let it bother me too much. The data in the first link is still applicable and correct, it just doesn't reflect the up the VAL coordinates that allow for the flare decreasing hole placement.
In many practical applications, there won't be a ton of difference in where the old P3 coordinates were VS where the new P3 coordinates would be.
On the old system, having a P3 would put it 2/3 the distance from your pap to the psa, and with a 6in measurement there, would put it 4in from your pap, while the new system would put it 3in from your pap.
Smaller pap to psa differences would mean smaller differences in the hole placement. Most balls are drilled with about a 4in measurement there, and would result in the hole only being off by approximately 2/3 in.
The P3 is still a flare increasing hole in either system, it is just that system #2 allows for a flare decreasing hole up the VAL, while system #1 didn't.