I just read all the comments in this thread and have a few of my own. First, I think Dave answered all the questions very well and completely (I love the idea of using Malus fusca for seedling rootstock! They are at least as drought tolerant and tough as the Russian Antonovika - though maybe not so cold hardy).
When I worked in an apple and fruit breading progam at the University of Arkansas, most of the fruit off of seedlings from crosses made 5-10 years before fruiting were pretty poor quality. But, once in awhile there was a good one and we selected it for some characteristic that might be useful, such as early to bear fruit, pest resistance, fruit quality, fruiting habit. On the other hand, when I was in graduate school at Rutgers University, I made 4 apricot crosses (crossing a great named variety with an OK tasting variety from Romania that blooms 2 weeks later and hence can beat late spring frosts). I got 4 seeds and 4 trees which I dug up and moved twice and replanted in Montana a third time 17 years ago. all 4 crosses produced excellent quality fruit that fruit regularly in Montana. But 2 trees are large and vigorous and 2 trees are small and bushy. It seems to depend on the variation, genetic plasticity, in the species you're working with. There is lots of variation in apple!
As far as taproots go, seedlings produce better taproots, but there are many examples of taproot trees doing well when tranplanted from deep containers such as "ray leach cells" or tublings. When I worked in mineland restoration, we had good to great success with oaks and conifers using 1" wide and 10" long ray leach tubes. Many of the trees planted 20 years ago are now doing well in harsh sites with no care at all after planting. Seeds are fun to work with, but the risk of getting a terrible tasting fruit is pretty high. If you have lots of room for lots of seedling, go for it.