You don't need to have it remove all of 1. You can model half of what you want, and have it remove that from the other log... so if you modeled up half of a bunch of your typical joints, it you take it out of the other piece.

I use this feature all the time on complex roofs, scarf joints, etc.
For roofs, I create cutting blocks and then subtract that out of the roof slab (usually on a valley or hip line). For scarf joints or other difficult geometry I create half of what I need, or even a series of blocks to make the cutting parts, then subtract it out.