200GB lost on APFS boot disk
The reasons for this problem were twofold, it has turned out.


About half of the missing space was in SIP-protected folders that are not found by programs like du or OmniDiskSweeper, not even when they are run as root. A safe boot fixed that.
The other half was indeed (see How to thin your local Time Machine Snapshots on macOS High Sierra mentioned in a comment to my question) in time machine local snapshots.


The LC_SEGMENT error may have been a red herring. Checking the APFS system with the machine in TDM attached to another Mac did not notice any problems with the file system.

Time Machine does provide a risk for boot file systems that are pretty full and that have a volatile content (large size of additions and removals). And these days, you cannot turn local snapshots off anymore.