Are Keep outs with height (3d keep outs) essentially keep In?
It can serve multiple uses. The first normally being a check that 2 components 3d models are not intersecting. 

Take a common mode choke. The size on the pcb for the footprint may be smaller than the component

Other things are enclosure design. If your board is meant to slide in some slots then you may add a ceiling to the pcb to ensure nothing will scrape or hit.

And finally it can be for planning. If things wrap around one another say with a folded sheet heatink you might extend the 3d constraint to leave enough room to both fit the piece and be able to tighten the screws.