I believe that DBI and DBD::mysql will not allow you to combine distinct statements (e.g. with an SQL string containing ";" to delimit two or more separate operations) in a single prepare.
But I expect it would be fairly simple to set up the perl script so that it reads a template, splits it into its component single statements, and then prepares and executes each in turn. That way, the templates themselves don't need to be changed -- you just need to be scrupulous about how you employ them within a perl script.
But then, I've never used mysql templates, and have never even seen one. If you can provide a simplified example of what such a template would look like, this would be instructive.
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