Hi Uffe,
Like you, having delved into TAM, I'm a bit concerned about some of the current functionality (and more particularly, the UI).
However, from my (still limited) knowledge of TAM, the export is working correctly. The uncloned vertices are (and probably should) NOT part of the versioned folder. Consequently, the export should be the same as for a non-TAM package. I thought these days, the export exported "stubs" for the out-of-branch vertices. If you're saying the stubs are missing, then that's a bug.
The problem (as I see it) with what you are asking is that (as I said above) the uncloned vertices are in a different structure. If you force EA to export them as part of this structure, you are exporting a corrupted model. However, that having been said, there may be use cases where such an export is useful. Can you elaborate on yours?
Paolo