If you're using the out of the box structural steel framing families, you may have noticed you can't use join to get the beams to cut holes out of walls they travel through. This is due to the fact that join only works on a family where the geometry is visible on all detail levels. Since the provided families have different representations at each detail level they will not cut.
If you have a project where you need the intersection line to show up in elevation/section/3d, simply edit the structural framing family and delete the geometry you don't want (we always delete the filleted sweep as it makes the family, and the resulting joins, simpler). Then make the other 3d geometry visible at all detail levels. Then reload/overwrite and join away!