Refactored the code to create the package after the other work is completed. Used an alias to preserve the file reference after the folder's extension is changed:
tell application "Finder"
set theFolder to (choose folder with prompt "Choose source folder" default location (path to downloads folder))
set theResources to make new folder at theFolder with properties {name:"Resources"}
set theContents to make new folder at theFolder with properties {name:"Contents"}
move theResources to theContents
set thePackage to make new folder at theFolder with properties {name:"Package"}
move theContents to thePackage
set thePackageAlias to thePackage as alias
set the name extension of thePackageAlias to "tblk"
set theConfigurations to (choose folder with prompt "Choose destination folder" default location (path to desktop folder))
move thePackageAlias to theConfigurations
end tell