The only advantage I can think of at the moment is that known rootstocks have been chosen to give predictable final sizes for the fruiting trees. So in a monoculture orchard you can plant the trees Xft apart to give good spacing for the grown tree. However, the scion also will affect the size that the tree grows to, so unless you plant only the same variety of fruit (all golden delicious
apple or all morello cherry for example) then even this advantage is lost a bit. There may be a case for using a rootstock with a known disease resistance, as I believe they do for grape vines in some areas, but I don't think these have been selected for top fruit trees as yet.