To create a secure MySQL Server environment, it is crucial to restrict the number of OS users that have access at the OS level (to prevent unauthorized access), ensure appropriate file system privileges for OS users and groups (to protect files from unauthorized access), and minimize the number of non-MySQL Server-related processes running on the server host (to reduce potential attack vectors and resource contention). Encrypting the file system is not a substitute for proper file system permissions, and running MySQL as the root user or keeping the software stack on one OS host does not inherently contribute to a secure environment.