I think you’re asking why you get two Machines when you specified cpus = 1?
That configuration is for the specs of each Machine. What you’ve got means “every Machine should be a shared-1x-256mb Machine”, where 1x refers to the number of vCPUs.
You get two Machines because fly launch tries to set you up for (somewhat) high availability. If you’d like to run just one Machine, you can fly scale count 1. You can’t specify number of Machines in your fly.toml yet.