Keeping difference when synchronizing

[fpemud]

I want to sync system config (mainly files in /etc) between my workstation and my notebook.
Generally speaking, it's simple and there's already many solutions.

But you know there's many small difference between the config of the two systems.
*** I want to keep the difference while doing full-automatic sync ***

Use make.conf as an example:
1. USE flag "doc", "examples" is workstation only, because the notebook's HDD is small.
2. USE flag "bluetooth", "v4l" is notebook only, because there's no bluetooth or webcam hardware on workstation.
3. When I add USE flag "gnome" or "kde", add it once and auto-sync it to the other side would be perfect.
4. But when I add USE flag "ieee1394", I need to tell the sync program by some interface that it's another notebook only USE flag so don't sync it.

I used to think conduit can do this, but after some learning I know conduit is more of a sync platform.
It's very flexible, but it doesn't provide this function by itself.

Is there any program can do this? (I highly doubt it)
Do you think its doable to implement one? (an idea: user provides a diff result, sync anything not in it)