My concern was that if Mastodon was its own server I'd have to run two servers in parallel, but since that's not the case, the question is a bit moot.
I'm so used to Apache+PHP+MySQL that in my little world nothing else exists 🤣 Although I do currently deploy to MariaDB, but since they're 99% compatible I've never had to bother enough with the differences to switch to MariaDB locally.