Thomas uses metaphor to interpret the prophecy. This is the correct method of interpretation, but it is not literal. Either he must concede that a literal rod will grow... or that the method of the apostles was to use metaphor in interpreting the prophecy. The difficulty in such a concession is that Thomas does not know how to discern between free-for-all metaphor and the methods that the apostles used so that their interpretation was not free-for-all. It is much easier to say that metaphor is part of literal and ignore the question of how meaning is derived from metaphor.

Why is the name 'Jesse' used if the prophecy applies to the offspring of David? Jesse had other sons. Would their offspring have sufficed to fulfill the prophecy? Because we have not been permitted to read the scriptures like the apostles, this has become a rather useless prophecy. All it says, even permitting the metaphor that a rod is a son, and a branch is a son, is that a son of David will rule. How many of the kings of Israel were sons of David? They could all use the prophecy to justify their decrees as being righteous whether they were or not.

Furthermore, Jesus did not rule as a literal king.