Flush inside is often specified for tanks with floating roofs, or in your case air raising roofs, so the seal is allowed to seat well. But, because the difference in shell thickness is usually no greater than 1/16", the offset of a center line stacked shell from course to course is only 1/32"- I don't think 1/32" is enough to make a difference. The weld profile if greater than 1/32", local shell deviations are commonly greater than 1/32". It's advantageous to use center line stacking during design/fabrication due to the common plate length for all shell courses rather than each course shell plate becoming successively smaller (by about a 1/16").