How to convert FusionDrive to APFS?
Well, my experiments have found an end, here are my ideas:
the origin of the error -69854 seems to be that there is not enough storage space. 

After another failed attempt installing MacOS Mojave from the USB, I went into the local Recovery Mode, before downgrading, and see: "Convert to APFS" in DiskUtility was not greyed out. It failed, as expected, with the -69854 error. When booting from the USB, the option there was clickable too, but leading to the same error. 
After moving and deleting some stuff to make more free storage space on Macintosh HD, the "Convert to APFS option" suceeded! Afterwards, installation of Mojave from the USB suceeded too. 

But to answer the rest of my question, after some more research:

To convert to apfs: diskutil apfs convert &lt;Name of the Disk&gt;. The correct disk seems to be – in my case – /dev/disk2 according to the Details of the DiskUtility. DiskUtility itself uses /sbin/apfs_hfs_convert – use man apfs_hfs_convert in Terminal if you want to learn more about that one.