If I understand the relationship, in the Jobs era Steve would give a design goal and it would be up to the engineering and the design team headed by Jony to work together to make it happen and make it pretty - Ive was in charge of the exterior design and likely consulted on the actual interior layout of parts.
After Jobs death Ive was promoted to oversee both teams, which is likely how something like the butterfly keyboard came to pass - Ive wanted thin above all else and the engineering teams had a lot less power to disagree