You can have a mixture of MyISAM and InnoDB tables in your database, so transactions will only apply to the InnoDB tables. Don't call it "failure", call it a MySQL "feature" :-) (BTW, DBI has nothing to do with it).
Update: I sense a misunderstanding of the relationship between DBI and the underlying database. DBI "knows" when you have the AutoCommit attribute set or not, so it can warn you when you do commits and rollbacks with AutoCommit unset. DBI doesn't "know" which of your MySQL tables are using the MyISAM or InnoDB engines on every SQL statement, so it can't warn you about that (the DBD::mysql library, with a bunch of extra work, might be made to do that, but it's really too much bother).
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