How to spawn an object while keeping the nested prefabs of this object?

Question

Unity

The situation is this. I'm writing a level generator. In order not to write the spawn of each repeating element in the level, I created a template and spawn it with the usual Instantiate () on the stage, for subsequent customization and turning the already configured level into a prefab. But when installing, the prefab label drops from all nested objects and they become ordinary game objects, which is very bad, because when you change some object, it is necessary that all elements in the levels change too. In this regard, the question is, is there a way to spawn an object into the stage in such a way that nested objects remain prefabs?
How it spawns now

How it needs to spawn

The line of code in which the installation takes place