The shutdown time assert was caused by untimely deactivation of
the binlog background thread and related structs destruction.
It could specifically occur when a transaction is replication unsafe
and has to be completed with a ROLLBACK event in binlog.

This gets fixed with the binlog background thread stop relocation
to a point and user transactions have been completed.
A test case is added to binlog.binlog_checkpoint which
also receives as a bonus a minor correction to reactivate a MDEV-4322 test
case that originally required a shutdown phase (that ceased to do).