I think the main difference is the organization controlling the genetics of the strain. MOA seeds originated from or are the seeds obtained from the Jamaican Ministry of Agriculture by Steve954 and distributed by Jamison. I would imagine the Jamaican MOA selects the peppers to propagate based on characteristics that they feel are native to the strain, pod shape, color, etc. As people in the states continue to propagate and resell these seeds, we may drift from the source strain.
If you buy a general scotch bonnet seed, you may not get as consistent characteristics since there is no organization controlling the genetics.
Someone correct me if I am wrong.
The recently imported seeds by Juanitos are controlled by CARDI, the Caribbean Agricultural Research and Development Institute. To be consistent with the MOA naming scheme of including the source in the strain name, should we be calling these CARDI Scotch Bonnets? I'm exited about these seeds because they are obtainable given the proper permits and wait times. This could help prevent any strain drift that we may see with people propagating the MOA seeds.