That was me when I was much younger. Basically I used a lot of cognitive dissonance. Yes, I was a biblical literalist. It was the word of God and the word of God needs to be perfect, not allegory not metaphor.

Would love to tell people I left because of some profound revelation but it didn't happen that way.

It's one of those things that could mean a lot or could mean nothing. Me personally I think it was a very important detail, because it means

1. The author had seen both methods used and picked the dramatic effect one despite knowing that earlier writers hadn't chosen that way.

2. Since he has Thomas stick his fingers in the hole it weakens the Thomasian/Gnostic view of the events. Indicating that Gnostics were older than expected, since there is no reason to rebute an argument with powerful symbolism if no one is yet making it.

In an alternate universe Peter is dubbed the Nail Puller of the church and never stops talking about how this one time he pulled some nails out.