I tried to reproduce on upstream MySQL 5.6.17 again, but now with workaround the missing root user problem:
* removed datadir contents
* mysql_install_db --user=mysql
* overwritten the user.frm user.MYD user.MYI from another 5.6.17 instance having root@localhost 
* started mysqld
* logged as root - no crash happens

Error log from the mysql_install_db stage:

2014-06-02 08:11:50 22015 [Note] InnoDB: Using atomics to ref count buffer pool pages
2014-06-02 08:11:50 22015 [Note] InnoDB: The InnoDB memory heap is disabled
2014-06-02 08:11:50 22015 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2014-06-02 08:11:50 22015 [Note] InnoDB: Compressed tables use zlib 1.2.3
2014-06-02 08:11:50 22015 [Note] InnoDB: Using Linux native AIO
2014-06-02 08:11:50 22015 [Note] InnoDB: Not using CPU crc32 instructions
2014-06-02 08:11:50 22015 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2014-06-02 08:11:50 22015 [Note] InnoDB: Completed initialization of buffer pool
2014-06-02 08:11:50 22015 [Note] InnoDB: The first specified data file ./ibdata1 did not exist: a new database to be created!
2014-06-02 08:11:50 22015 [Note] InnoDB: Setting file ./ibdata1 size to 12 MB
2014-06-02 08:11:50 22015 [Note] InnoDB: Database physically writes the file full: wait...
2014-06-02 08:11:50 22015 [Note] InnoDB: Setting log file ./ib_logfile101 size to 48 MB
2014-06-02 08:11:50 22015 [Note] InnoDB: Setting log file ./ib_logfile1 size to 48 MB
2014-06-02 08:11:51 22015 [Note] InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
2014-06-02 08:11:51 22015 [Warning] InnoDB: New log files created, LSN=45781
2014-06-02 08:11:51 22015 [Note] InnoDB: Doublewrite buffer not found: creating new
2014-06-02 08:11:51 22015 [Note] InnoDB: Doublewrite buffer created
2014-06-02 08:11:51 22015 [Note] InnoDB: 128 rollback segment(s) are active.
2014-06-02 08:11:51 22015 [Warning] InnoDB: Creating foreign key constraint system tables.
2014-06-02 08:11:51 22015 [Note] InnoDB: Foreign key constraint system tables created
2014-06-02 08:11:51 22015 [Note] InnoDB: Creating tablespace and datafile system tables.
2014-06-02 08:11:51 22015 [Note] InnoDB: Tablespace and datafile system tables created.
2014-06-02 08:11:51 22015 [Note] InnoDB: Waiting for purge to start
2014-06-02 08:11:51 22015 [Note] InnoDB: 5.6.17 started; log sequence number 0
2014-06-02 08:11:51 22015 [Warning] Bootstrap mode disables GTIDs. Bootstrap mode should only be used by mysql_install_db which initializes the MySQL data directory and creates system tables.
ERROR: 1787  When @@GLOBAL.ENFORCE_GTID_CONSISTENCY = 1, the statements CREATE TEMPORARY TABLE and DROP TEMPORARY TABLE can be executed in a non-transactional context only, and require that AUTOCOMMIT = 1.
2014-06-02 08:11:51 22015 [ERROR] Aborting
  
2014-06-02 08:11:51 22015 [Note] Binlog end
2014-06-02 08:11:51 22015 [Note] InnoDB: FTS optimize thread exiting.
2014-06-02 08:11:51 22015 [Note] InnoDB: Starting shutdown...
2014-06-02 08:11:52 22015 [Note] InnoDB: Shutdown completed; log sequence number 1625977
2014-06-02 08:11:52 22015 [Note] ./bin/mysqld: Shutdown complete
  
2014-06-02 08:11:52 22038 [Note] InnoDB: Using atomics to ref count buffer pool pages
2014-06-02 08:11:52 22038 [Note] InnoDB: The InnoDB memory heap is disabled
2014-06-02 08:11:52 22038 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2014-06-02 08:11:52 22038 [Note] InnoDB: Compressed tables use zlib 1.2.3
2014-06-02 08:11:52 22038 [Note] InnoDB: Using Linux native AIO
2014-06-02 08:11:52 22038 [Note] InnoDB: Not using CPU crc32 instructions
2014-06-02 08:11:52 22038 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2014-06-02 08:11:52 22038 [Note] InnoDB: Completed initialization of buffer pool
2014-06-02 08:11:52 22038 [Note] InnoDB: Highest supported file format is Barracuda.
2014-06-02 08:11:53 22038 [Note] InnoDB: 128 rollback segment(s) are active.
2014-06-02 08:11:53 22038 [Note] InnoDB: Waiting for purge to start
2014-06-02 08:11:53 22038 [Note] InnoDB: 5.6.17 started; log sequence number 1625977
2014-06-02 08:11:53 22038 [Warning] Bootstrap mode disables GTIDs. Bootstrap mode should only be used by mysql_install_db which initializes the MySQL data directory and creates system tables.
2014-06-02 08:11:53 22038 [Note] Binlog end
2014-06-02 08:11:53 22038 [Note] InnoDB: FTS optimize thread exiting.
2014-06-02 08:11:53 22038 [Note] InnoDB: Starting shutdown...
2014-06-02 08:11:54 22038 [Note] InnoDB: Shutdown completed; log sequence number 1625987