It's not a weakness, it's better than without support for it.That's definitely a weakness of sky3ds that for a game to work it needs to be in the template file first
The template data can be edited, but you need some values from a real cart, it contains "cartridge id", "unique id" and other values + checksums.And you can't edit the template with the required information?
Most of the data can be generated from a normal rom file, but unique id can only be dumped from a real cart, it's the same id that .3DZ uses for online play.