Could I set my InnoDB MySQL Server session state for SQL_SAFE_UPDATES and INNODB_FLUSH_LOG_AT_TRX_COMMIT?
What version are you running?  5.6 doc gives the details:

innodb_flush_log_at_trx_commit can be set (1) on the commandline, (2) in my.cnf, or (3) via SET GLOBAL.

sql_safe_updates can only be set via SET SESSION or SET GLOBAL.

Note that SET GLOBAL does not impact anyone currently connected (including yourself).  It will effect anyone connecting later, but before the next shutdown of mysqld.

my.cnf affects those who connect after the next restart.

Your question asks how to set them, but fails to say what the ultimate goal is, so I cannot recommend a particular approach.  (Do you care about Workbench?  Your C# connection?  Others currently connected?  Future connections?  What?)

I do not know whether Workbench re-connects between actions.  It probably does.  This implies that SET SESSION may not have any impact.

Update (based on update to Question)

SET GLOBAL INNODB_FLUSH_LOG_AT_TRX_COMMIT = 2;
Note: that SET will affect other users.
Now disconnect and reconnect.
SET SQL_SAFE_UPDATES = 0;
and do the rest of your task.


But...  Neither of those settings impact a mere CREATE TABLE.  I assume you will proceed to do INSERTs and UPDATEs?

Side notes:  These two indexes are redundant and should be removed:

UNIQUE KEY `ASID` (`ASID`),
KEY `IX_ActionSequence_EAID` (`EAID`),


A PRIMARY KEY is a UNIQUE KEY is a KEY.

Why have both ASID and EAID?  Both are UNIQUE; both are VARCHAR(64); either could be the PRIMARY KEY.