You can create a local or shared directory for the shared configuration files in highly available environments.
Do not use one of the cluster servers for the file location as this creates a single point of failure. The bootstrap.properties file could, theoretically, be placed on a local Windows share or local NFS export directory from any of the systems in the Application Engine/Workplace XT cluster (that is, shared out from the default file location from the first installation). However, if the local system holding the file would go down, other Application Engine/Workplace XT instances will be unable to find the bootstrap.properties file and will return error messages.