Any moderately complex app has a few moving parts. At least you have the web server and the DB. The DB has settings like the default character set, table types etc. These have to be kept in sync across all instances, dev, stage, and prod. The web server also has modules and a conf file with mod_rewrite rules which change and should be kept in sync. Sometimes you update a library or a version of ruby. Add a noSQL server, message bus, file storage, email, etc and you can see how it becomes a serious issue. And the problem grows exponentially the more developers there are each with one or more dev instances which have to get the latest changes and be kept up to date.

These things all have to be dealt with and should not be thrown over the wall and "let the sysadmin deal with it." That's where the value of the OS and infrastructure is a set of code and config files which are kept in source control next to our code and versioned with it is so valuable. Run "vagrant up" and a fresh consistant build every time. Then develop in php, python, perl, ruby or brainfuck if you want.