Hello,
This looks like a really cool mod! I've found a little bug while trying to see how it works in Editor mode. When you deconstruct something using the deconstruction-planner (in editor mode) then the hidden entities beneath still remain. The deconstruction planner does work in non-editor mode though.
As a side note: I couldn't figure out how it works. Your mod page has a lot of information but it doesn't say how the actually transformers work and what to connect to what. It might be worth adding something like a minimum viable example of how it works. :)