When the column feature is used in the email template builder, the alignment changes between the change from the editor, to preview, and then on to send. Although the alignment is barely off centered, when the rest of a email perfectly formatted and centered it becomes quite clear.
After reaching out to support I was informed that this is a limitation, and the only solution was to use the table rather than the columns feature. The issue with this "solution" is that tables are formatted the same between desktop and mobile views, where as the columns feature is dynamic and adjusts for mobile viewers.
I would assume that anyone who selects for their columns to be centered expects it to align to the same center as the rest of the email template builder components.