Chances are that you don't have a mixed fleet for a particular application though. So if you have a bunch of FizzBuzz VMs that you need to bring online, you can safety write shell scripts that work on FreeBSD because you know all FizzBuzz machines will be running FreeBSD. If you've also got your BazQux service that needs a Linux fleet, then for that fleet you create shell scripts that work on Linux.

There may be some overlap between things that must be done on both the FizzBuz and BazQux fleets, but that overlap is probably in simple tasks.