I'd say the "-R" might actually be harmful; for example the mysql GPL distribution binaries from dev.mysql.com installs in /usr/local/mysql and you definitively

I'd say the "-R" might actually be harmful; for example the mysql GPL distribution binaries from dev.mysql.com installs in /usr/local/mysql and you definitively don't want to mess with the database file permissions there. It might not be "best practice" to let non-homebrew stuff put things in /usr/local, but it happens.