This is an interesting process and I want to thank you for sharing it.
Assembling the feature separately seems a bother and doesn't follow a particular known process.
I would associate your implementation in how I do clinched inserts, where the case is a standard process.
In Creo, the intent is to use the die features within the fab part file rather than the assembly.
This is easily done in one of many ways. I would venture to guess that an industry that uses this feature a lot could use the die set in a feature library (dies).
But the question seems to be how to manage these at the next level assembly. How to show the deformation of the joined surfaces.
My 1st instinct would be to ignore it. Having the features there lets you account for them visually but the deformation may be moot as the space claim is reduced. If this is a 10,000 to 1,000,000 features per year in CAD, I might opt for non-treatment at the assembly level. If I need a detail for the drawings, this too can be a library "image" rather than a true section on drawings.
If I had to do it, I would ask myself how I would show a clinched standoff's threads in one level and not at another. Now my options are quite limited. (this is not a real use-case for me, but analogy is the same.)
You definitely have two different features. Meaning you have to model them both to show them both.
I'm afraid the only way I see this working is with family tables. However, if you can treat the original die feature with additional processes, then you can suppress these in the fab drawing (visual state) where they would default to "as processed" in the master representation. I don't like family tables personally. But this visual state where you can remove features is quite handy. Normally, I want the master rep to carry forward in the assembly process. Sheet metal doesn't really help with this leaving the flat state as the default rep. This too requires hoopes to be jumped through.
Let me know what part of this is not clear and I will clarify.
