mysqld started by mysql_install_db will hang when having log-bin in config file

I'm installing with a custom setup script and a my.cnf template that has "log-bin" in it from the very start.

This makes mysql_install_db, or actually the bootstrap mysqld process, hang.

The last line printed before hanging is

2016-08-11 12:13:04 140389765464832 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1146: Table 'mysql.gtid_slave_pos' doesn't exist

strace shows mysqld hanging on:

 futex(0x560b65c2db44, FUTEX_WAIT_PRIVATE, 1, NULL