You don't need to make MySQL installation InnoDB - Just the Stash DB.
Just add "ENGINE = InnoDB" for create database SQL query.
https://confluence.atlassian.com/display/STASH/Connecting+Stash+to+MySQL
It's fine to do that in JIRA, can't see why not in Stash either, as long as you make sure the tables created in the Stash DB will use InnoDB I can't see a problem.
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