All .plist files that come with Formulas can be found in Cellar dir. For instance homebrew.mxcl.mysql.plist is in /usr/local/Cellar/mysql/5.7.14. You can modify it and brew services will use it.
Alternatively you can modify /Library/LaunchDaemons/homebrew.mxcl.mysql.plist and make it immutable with sudo chflags uchg /Library/LaunchDaemons/homebrew.mxcl.mysql.plist. This won’t allow brew to rewrite or modify .plist file.