Work around for nested prefabs? (for my use case - random levels)

I am aware that this has been a common problem for a long time (why has Unity not done anything about it yet? sigh) but I am currently working on my first project that is large enough for me to even notice that this problem existed.

I have found a couple of workarounds already but I don't find them especially useful for my current situation.

I am creating a game that has 'randomized' levels - basically I am creating many small sections of levels and they will be spawned in a random order. Each level section is a prefab (of an empty game object), with many prefabs as children for enemies and obstacles etc. Unfortunately, all the references to the enemy prefabs are lost, and I am finding that if I want to change something about an enemy I must go through every instance of it in the level sections and change it manually, which is fine for now since I have a small handful of level sections but obviously this will be incredibly painful as the project grows.

I found this solution which essentially is a dummy gameObject that spawns the prefab at runtime, which would be fine, apart from the fact that it doesn't allow for overriding properties (and I need to be able to do this for my game unfortunately).

I also found this in the asset store, however the reviews suggest it is far from bug-free and I don't want to just change my problem into working around the bugs in this tool, not to mention waste my money on a tool that isn't stable.

Has anyone had a use case like mine before? How did you work around it?

Thanks!