Good questions.

If 'Father' and 'Son' were one why the distinction.

They are separate persons that share the same essence/nature. Difference in roles, but holding the same office.

Joseph didn't understand what young Jesus did

Yes, it was difficult for early Jews to understand who Jesus was, even his family. Even Jesus said “a prophet has no honor in his hometown.”

God was progressively revealing himself at the time in the flesh (Messiah), which was foretold in Hebrew prophecy, but the Jews still had a hard time reconciling what they were seeing with Jesus. More miracles (revelation) were needed.