While at the current point in time there is very little difference, and maybe no difference at all, this is a bad practice if your development environment supposed to replicate the server your code will run on.
There is just no point in forking a product without having the intention to change it, and the changes might be explicit as different toolset commands or SQL syntax changes, or hidden like better/worse performance for some queries.
For 99% of the wordpress oriented development it makes no difference, but it always sucks to discover your current specific project is in the 1% only when you are running into problems (which usually comes when you have no time to waste on such things).
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