When executing an ALTER TABLE, InnoDB (and XtraDB) will create two InnoDB transactions:
This will show up as something like “TABLE LOCK table `schema`.`table_name` trx id XXXX lock mode S” in SHOW ENGINE INNODB STATUS.
A little known fact is that the InnoDB data dictionary is somewhat transactional (the big thing it’s missing is any form of MVCC. It’s not ACID). The largest part of ALTER TABLE not being completely crash safe in MySQL is the MySQL server manipulating FRM files.
The only MySQL storage engine I’m aware of having fully crash safe DDL is MySQL Cluster (NDB).
Proving that MEMORY is/isn’t crash safe around DDL is an exercise left to the reader 
Thanks go to Alexey Kopytov for looking into the InnoDB code for this post.