Prebuilt gameobject bundles without Prefab instancing behavior.

I've built a system for my game that involves several different game objects all interlinked- it's a terrain object and a grid tile object that are tied together with several scripts. I'm looking for a way to bundle this system together so I can use it in several scenes.The ideal behavior here would be that I could create a new 'ground' object, and it will instantiate with a default terrain grid and terrain data that can then be edited up to how I need them in a given context. I've tried doing this with prefabs but have found that when I do, the terrain data and the tilemap data can't be overridden in the various instances of the prefab. I also can't make prefab variants for each context, because the terrain data and the tilemap data persists between variants.

Anyway, I'm wondering if anyone has insight into how I could go about doing this. I understand that it's a bit of a pathological use case, but it seems like it should be possible. Am I missing something that would easily unlink the instances of these objects as prefabs? Are prefabs the right tool here at all, or should I be dipping into some other toolbox?