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If encryption at rest (EAR) is enabled, all files transferred to CompleteFTP are stored on the server in encrypted format. How can I get access to the unencrypted files for local external programs?

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The only way you can get access to the unencrypted files is via a user account on the server - that's by design. There are three options:

1) You could login using a client program and do a local file download to the destination where you want the files. That will decrypt the file. 

2) You can decrypt files by logging into the server via command-line ssh and using the decrypt command. More here. Note that as it is an admin command, the user must belong to the admin group on the server. 

3) The following JSS script can be placed in an upload process trigger.  It decrypts the file immediately after it's been uploaded:

var filePath = event.virtualPath;
var decryptedFilePath = event.virtualPath + ".decrypted";

// copy decrypted content to anotehr file
system.executeCustomCommand("decrypt", ["-s",filePath,"-d",decryptedFilePath]);

// delete the decrypted file

// rename the decrypted file to original name