Dunno if anyone's swapped their Ironhide's shoulders... but i ended up swapping his back and doing Ratchet's instead tonight.

The shoulders looking better are definitely a red herring! Basically, the piece that people have been swapping has a screw tube coming out of it, 90º to a hollow slot beneath it. If you look directly at the hollow slot on both pieces, you can see the screw tube isn't dead centre, it's offset by... exactly the size of the gap that appears when you have nice shoulders.

You can see the difference again when you place his arm back onto his shoulder. Have it almost in car mode and look at Ratchet's right arm, with the front window swung up. With Ratchet's cross facing out towards the side of the car, look at the right side of the shoulder block. That piece has a wedged angle, that will either line up with the end of the shoulder joint above it (gap, pretty shoulders), or sit the offset amount to the left (no gap, ugly shoulders)

The reason some people have gaps on one side and not the other after making the shoulders pretty is simple... You can't slide his arm since it's offset, so you have to twist the arm to get one side looking good. Doing so pushes the other side out more, since the shoulder blocks are supposed to be right up against each other, but instead one is angled.

Seems to me based on that, that it's Ratchet who is misassembled, though really what you choose to do is up to personal preference!