I know you cannot use DiskWarrior to rebuild the Mojave directory on an internal drive. I am able to Carbon Copy clone an external drive (in my case, an SD card) from my Mojave system and I can use DiskWarrior to rebuild the directory of the external drive.
I asked DiskWarrior tech help if cloning the external drive back to the internal drive would be the same as a directory repair. They said:
"Cloning a disk does not make a directory repair. It simply makes a new directory. This may solve some problems, but not all."
So, until the next major iteration of DW is able to cope with APFS drives, this is better than nothing. I guess.
I've been using DiskWarrior and TechTool Pro since OS 8.5. Can't get out of the habit, but maybe Carbon Copy Cloner is all I really need now.
It seems to me the DW tech person did not fully understand your question. You said you cloned,
repaired with DW, then cloned back. Would the cloned back directory still have the repairs? Why not? The tech only said cloning fixes some problems, not all. You cloned and repaired.
