I don't know any frameworks that do it, but it seems like you could have an element that fits into the normal grid, and then inside that have an element with a "breaks the grid" class applied which uses positioning raise it up and make it overlap grid boundaries. You might need a special class on the parent element too so you can prevent it from collapsing. This seems like something that can be done in a fairly generic way.
Yeah, I think in isolation stuff like that can be useful, but I feel like there should be a better abstraction. I'm not enough of a designer to know what that abstraction would be, and it seems like unexplored territory in CSS frameworks now as far as I can tell.