I'm not sure you are using the correct terms. Propagating by seed and propagating by cloning does not give identical results. Propagating by seed gives you a genetically different tree. Therefore it is not a clone of the parent.
Propagating by cloning gives you a new, genetically identical plant. Sometimes too identical (as explained below).
Rooting clones are made by dividing the roots. Each separate root becomes its own identical (cloned) tree.
Tissue cloning takes a cell of a plant, tests are done to verify the cell has no viruses, and then the cell is grown into a plant (virus free).
The difference between M7 rootstock and EMLA-7 rootstock is that EMLA-7 rootstock in grown from an M-7 rootstock clean of pathogens (bacterium, virus, or other microorganism that can cause disease). When transplanted the tissue cloned tree will pick up pathogens as any other plant but in its beginning it is very healthy, strong, and vigorous.
So to answer the question "Are there any drawbacks to clonal propagating roots of seedling rootstock?" The answer is, yes. As described above. But if you don't have a laboratory to grow your roots cells in --free of pathogens-- then root propagating is your best method.
So, if you will want to multiply your rootstocks all you have to do is separate them and you get a clone. There are several ways to do that that is google searchable. Many nurseries do this to save the money on buying rootstocks. If you only want a few (to a few) dozen trees you usually save time by buying the rootstocks and grafting your own trees at a minimal cost.
I hope this helps.