I don't know anything about IS-U, so I might be off on this, but based on the limited information in your post and in the note 1810101 on Improvement Finder site I don't see much logic in the SAP response. It could be respondent's Yoda-like grammar or some translation issue, but I don't get at all why adding a change document is "a difficult point" and what security has to do with it.
If the 'Change document' checkbox is checked in SE11 then the change document should be created. The whole "difficult" development is to call a function module, as far as I recall. Not a rocket science. The argument "there is no error because it is based on our very bad design and we were too lazy to add a few additional lines" seems rather laughable.
The Improvement Finder page does not say anything about specifically excluding change documents. It just goes about the new functionality. I can only guess that change documents were not specifically put in the specification, but perhaps it was because it was just expected. E.g. we don't put in the spec that changes need to be written to the database, some things are just implied.
Even though technically it is not an error, personally I don't see any valid reason why this must not be done. Again, it's not my area of expertise, but I strongly suspect that the whole talk about the complexity is a brush-off. "Shorry, couldn't make it". 
P.S. I'm curious how this would work in "The Cloud".