Build in some form of support for integrity checkers (e.g. tripwire). One thing which has kept my from using any of the existing tools like linuxconf or webmin is that I always get some tripwire error messages about changed files.
This might even be implemented in the form of an additional backend which takes the list of modified files and feeds it to the tool that recalculated the checksums and updates the database; all with proper authentication of course.
Integration with tripwire/aide/etc is certainly not a pressing goal, but it is a great idea. We're planning to have the middle layer log changes in some way(including what files were changed) and there are a lot of good reasons to make optional components available which do other things with config changes (modification detection, copying to multiple boxes, creating a script to get from state A to state B, etc.). To do things like managing users, changing hard drive settings, etc. it may turn out that this type of change to set of commands translation is necessary.
You have some good ideas, and we will try to make it so that even if we aren't able to implement and stabilize all the requested features, it will be relatively easy for people to add them later since our system will be as modular as possible.
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Since hardcoding stuff is depreciated, providing simple hooks for such tasks seems OK. Possibly as simple as pre-cfg/post-cfg shellscripts.