Okay, I figured out the "Conflicts" part of my question above -- you have to actually enable the mod before the conflicts show up, but the step telling you to do so is not until much later in the guide. There's another gotcha related to mod cleaning, which is "xEdit Output" has to be enabled for cleaning to work, otherwise it complains about the directory not being writable.
Also, the instructions to download the Step Patch - Conflict Resolution seem to be missing. I managed to find it by searching on Nexus, but the only link is "Don't forget to endorse Step on the Nexus if you like the guide.", which is extremely unclear.