I wanted to get a better understanding of the Rhino Scale Command.

If I have a square at 6.5 all sides and another square at 3.25 all sides then click both to scale proportionately and scale the 6.5 by an increase of 1 to 7.5… the small square becomes 4.75. Shouldn’t the small square be 4.25 to maintain the relationship to the starting dimensions and not necessarily each other?

Scale factors work by multiplication, not addition. When two different size objects are scaled by the same factor the ratio of the size of the objects remains the same (size A / size B), not the difference (size A - size B).