Yeah, it's quite confusing.
One option controls the base size of icons in a group. The other sets a multiple of rows or columns the individual icon can cover. If the icon can cover 2 rows and 2 columns then the icon will be more than 4x as big (more due to the text getting the same space on both so a smaller percentage of larger sizes). When you think about it this makes sense as icons have to cover a whole number of lines.
Until more recent versions of Start11 the second option was for Windows 10 menu style only and on other styles you just controlled the size for all icons in a group. This additional option seems to have confused some people unfortunately.