Version control tools all still operate at the level of line additions and deletions, and don't accommodate data with structures that don't map neatly to those boundaries.
I think that certain very high-end "asset management" or "configuration management" tools like Alienbrain have things like Photoshop and 3D Studio Max plugins to do structured conflict resolution within an editor for structured content, but I have never had the opportunity to use one, so I'm not sure if or how they work.
This is one of the reasons I have always liked Bazaar; the pluggable back-end could hypothetically store any kind of content; the pluggable front-end could hypothetically invoke editors (GIMP, Photoshop, whatever) with appropriate plugins for merging and conflict resolution.
Unfortunately while the hypothetical consequences of Bazaar's mutability are great, the practical consequences are more problematic; years of format-migration bugs and headaches.