It's not the grafting that results in better fruit, it's the particular scion (the cultivar that you graft onto the rootstock) that produces the good fruit. If you graft a Red Delicious onto one of your sapling rootstocks, you'll get Red Delicious apples from the Red Delicious scion. If you don't graft a known good cultivar onto your rootstocks, you'll get "wild" (non-cultivar) apples. Those might be wonderful, but your chances are slim. You are more likely to get something not all that great. Grafting a seedling onto another seedling still gives you seedling ("wild") apples.

Another thing to consider is that the rootstock itself if often chosen for specific properties. One of the most often recognized is dwarfing rootstock's ability to control the growth rate (size per given amount of growing time) of the tree. A dwarf or semi-dwarf tree can be a lot easier to maintain and work with. There are also many other characteristics (soil and climate adaptability, etc, etc) that rootstocks can control. Using seedlings for rootstocks may be satisfactory, but won't provide the unique characteristics available with a custom rootstock cultivar.

Have fun with your seedlings, whatever you do with them, BUT don't count on them to produce the same quality/type of tree that you could expect from a choice scion grafted onto a carefully chosen rootstock.