You're right, what's for sale are are rootstock trees. But I believe you can get access to seed stock as well.
All the apple varieties you eat have been cultivated from a single original specimen, via cuttings or (more likely) grafting onto a convenient root stock.
I feel this warrants more research for me.
The story is also similar for rootstock. Apples are naturally a fairly large tree, which isn't convenient for harvesting. The rootstocks that apples are typically grafted onto are genetic variants that don't grow as large.