Splitting from T152394: BlockUser::log() creates a log entry and inserts it, without offering any way for callers to alter the entry. In particular, it is not possible to alter visibility of the entry (via ManualLogEntry::setDeleted), which has at least a use case (see mentioned task). Three possible solutions:

1. Add a setter for log entry visibility, i.e.

/** @var int|null */
private $logDeletionFlags;

/**
 * @param int $flags One of LogPage::* constants
 */
public function setLogDeletionFlags( int $flags ) : void {
    $this->logDeletionFlags = $flags;
}

private function log( DatabaseBlock $block, bool $isReblock ) {
     // ...
    if ( $this->logDeletionFlags !== null ) {
        $logEntry->setDeleted( $this->logDeletionFlags );
    }
    // ...

2. Add it as a constructor parameter inside $blockOptions
3. Add a hook to allow further customization of the entry

I would be fine with any of these solutions, keeping in mind that option (3.) might lack real use cases, and it would have to be considered as a long-term solution, whereas (1) and (2) can be introduced as a more hacky/temporary™ solution.

Tagging AHT per developers/maintainers.