I don't think anybody besides you will ever notice the difference in gun port position, as you show, only visible when looking straight down, and most models are not viewed from that angle.The last four cannon rigged up. You can see in the last picture a subtle difference in spacing between the second and third cannon on the starboard side compared with the port side. This is evidence of imperfect bulkhead fairing and imperfect planking. There is a very slight curve to the hull on the starboard side as opposed to the port side. After the masts and all the rigging is installed it will be impossible to see this imperfection, but I know it's there...and now you too I suppose.
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I don't think anybody besides you will ever notice the difference in gun port position, as you show, only visible when looking straight down, and most models are not viewed from that angle.