When executing an ALTER TABLE, InnoDB (and XtraDB) will create two InnoDB transactions:
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).