I think i had the same confusion once how that worked i long time ago, and i see its still the case
it presumes that you setup the stage with all your base objects
if you multiple instances, its not clear what the prototype is, its more a managing thing at that point
why they do it like this?:
in the end, i think its because its easy to set up initial value's for the prototype like this , so you dont have to specify or change certain properties manually, easy for testing like different sizes, etc..
on the other hand it could take and set basic default properties, then you change in code once created.. and trow away the need for instancing objects in the level editor , it would be more a standard way of working,
not sure if its worth changing it at this point..
perhaps a button that directly jumps to the prototype that will be used , is faster and easy