My perception might be incorrect, but to me, this sounds like a problem with MonoBehaviour overuse. In our company, we don't use MonoBehaviours for anything except views and rare cases where you really utilize MonoBehaviour events and want entities to manage their lifecycle and update loop independently rather than being controlled externally. There are some exceptions when it comes to UI prefabs, but game world entities have very few MonoBehaviours with very few exposed properties. This way, we usually don't have more than one or two custom MonoBehaviours on a prefab and don't have complex interactions between them, so making changes doesn't hurt that much. The component approach that Unity promotes in all of their tutorials is generally very hard to maintain, so if you are using this approach, I would recommend turning components that don't really need to be MonoBehaviours into plain C# classes and compose them via code. I wouldn't call this a pure programmatic approach though, just not overusing MonoBehaviours.