Hi all,
It is correct that this is currently a product limitation. Links are not decorated with tracking information if the link is inserted via email scripting. Our product team is aware of this limitation and it is something we'd like to resolve in the future.
Regarding sending sample emails, we are currently working on a bug fix so that links in sample emails will appear as if the email was sent as a production email (so you can see exactly what your lead(s) will see). Look for this to be released in the next one or two releases.
Thanks!