The "supported" version of MySQL is 4.1. I have read of some complications with MySQL 5, but almost certain those are unique to those encountering it. There are some improvements to MySQL 5.0, but none that I would say warrant breaking the Emulator over.
Basically, the best possible way to get your answer is to setup an emulator using MySQL 5.0 and see what happens. While testing is done during development, there isn't an official QA department that runs it through every possible iteration of software combinations. That comes from community trial and error.
Hopefully, not many errors.
