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..
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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