Our work with elite athletes serves as the proving grounds for our methods. Most people don’t play professional sports. But if our methods help athletes at the highest levels, they can work for anyone.
Seems like you’re having some issues getting your actual question answered. Not that everyone didn’t provide great resources and advice on the front rack archetype in general, but you seem to have a pretty specific question regarding protraction/retraction of the scapula that has yet to be addressed.
I would say, as the others have, that the more retracted shoulder position would be prefered, though I also find it difficult to avoid protraction when setting up the front rack. If you find, as I do, that you are unable to position your arm (flexion/external rotation) without pulling the scap forward (protraction), it might indicate that your posterior delts are stiff, thus pulling the scap forward when you position for the front rack.
Also, make sure you are addressing your set-up for the front rack (motor control, as someone mentioned previously). If you’re not setting up and creating torque through the shoulder in a good position before you load that bar up, it will make it very difficult to establish a decent front rack shape.
Hopefully that offers you a little insight into your problem!