This one passed me by in Revit 2014, but may have been picked up by others; you can now switch the join order of elements. This is probably best demonstrated when needing to join like minded materials together, such as concrete beams & slabs
Here we have 3 pre-cast concrete beams & a slab. We obviously want to join the elements together to create nice clean joins.
If we choose Join Geometry from the modify tab, we can select the slab & join it to the beams.
Now if we don’t want to show the beams projected into the slab as indicated in the image above, select the Switch Join Order tool, & the select the slab & then each individual beam to switch the way the concrete cleans up.
The cutting rules are recognised when you create a section box through the model as well. Here I have joined one beam so it projects into the slab, the other 2 remain flush to the underside of the slab.