Does the idea of parts of the Bible being allegorical or metaphorical contradict God's honesty?
What God said is always true in the way he intended. The error is that people often don't understand what God intended and then blame God for their mistake.
For instance, God says that he doesn't change. But Jesus was God, and he became a baby, who grew up. That is change. He moved around, that is change. When God said he didn't change, he was truthfully saying what he intended to say. Someone playing games with his words does not make him a liar.
Jesus's genealogy is in Matthew and it says that there were 14 + 14 + 14 generations. But there were only 41 names listed. Did he lie? No. He gave a riddle. Riddles and parables are truth masked to look like fiction.
The riddle of the genealogy is that "generation" comes from 'toledoth' and means record. As you look at the record of each man in the list you will find a picture of Christ. The first 5 are all second sons (Judah in riddle) then a block of only begotten sons and unbegotten only sons. You will also find the answer to the riddle posed to Jesus about the woman who had seven husbands. They are listed in the genealogy.
The missing record tells us that there is a hidden message in Matthew making the record of Jesus into two records. One will tell how he is the Son of David, and the other how he is the son of Abraham. The literal record shows him to be the king of the kingdom of God. The second shows how all the promises made to Abraham have been fulfilled.
A great disservice is done to the Bible when it's prophetic nature is denied and when riddle, as the language of prophecy is not recognized.
The second riddle in Matthew is that the angel said to name Jesus Yeshuah, and Matthew says this fulfills the prophecy that he would be named Emmanuel. Yeshuah and Emmanuel aren't the same name. Did Matthew lie? Or was it a riddle to teach us how to read the Bible? Yeshua means 'God's salvation' not 'God with us'. It is the pun of Yeshua that means 'God humbled' referring to his incarnation and the fact that he is with us. The use of puns will solve the mystery of the hidden prophecy that Jesus would be called a Nazarene.