I wouldn’t use a prototype as a container for other notes (say, prototype MyReference – based on modifications of the built-in Reference prototype). Instead, I would create a new note (MyContainer) to use as a container, and assign MyReference as MyContainer’s prototype.
Why? Because the children of prototypes also become the children of notes that are assigned that prototype. (Easy to test and see this for yourself.) In your case, you are “de-prototyping” the container so the risk of mistakenly creating notes you didn’t intend to create is low.
But unless you intend for a prototype’s child hierarchy to be inheritable, it’s not a best practice to use prototypes as containers, in my opinion.