When miracles like the stigmata exist, it is important not to get too technical with them. For whenever God communicates like this with mankind, He is condescending to our level. For example, at various Marian apparitions, she has had a different nationality specific to the receiver of the vision.
The reason why a stigmata may not appear in the identical spot as actuality is because it is not a duplicate representation. It is a sign, that God enacts on our terms. For example, when Padre Pio would get pains on certain feast days, it did not mean the feast’s occasion had to have happened on that exact day. However, because the pain came on the day Padre Pio understood as a feast day, the event took on meaning related to that feast day. The same way, the Stigmata having come via the hands and feet, which is how the event had historically been presented, thus brought with it mankind’s understanding that this is a participation in the suffering in the cross. But, I wouldn’t be surprised, because of our more modern forensic studies, if a stigmata appeared in the wrists in the coming centuries.
We should also acknowledge, as other historians have speculated, if Jesus was crucified through the hands it could have been possible depending on nail placement or the use of ropes like in the movie The Passion of the Christ.
You can see other examples of God’s condescension to human levels in His very Incarnation, Scripture written in human language, etc… Some Scripture accounts vary from writer to writer, like the 3 different accounts of healing Peter’s mother-in-law.
God’s ultimate representation would be as pure spirit. Yet we can connect with Him as such, being ourselves finite. The point with the language of Scripture, or a miracle, etc…is to determine what God is trying to communicate through our mechanisms of communication.