Recurring Volume damage + Time Machine issues
Not much of an answer, but I eventually solved both this issue &amp; also Notification Centre - What happened to Calculator widget? by cloning the drive, reformatting to HFS+ &amp; cloning back again.  

No amount of messing with APFS would fix it.

Late Edit:
Some time later I now have two of the ABA/ACA &amp; the odd one out, an HDWQ Toshiba drives giving the odd "Volume [name] on disk4s2 has 0 bytes of trailing loader space and it needs 134,217,728 bytes" error.
Always that precise number.

Late Late Edit:
All this trouble went away with Mojave [mainly]. I have found that periodically I need to run DiskWarrior over the Time Machine drive, if anything starts to play up, but only every 6 months or so.