Hi, I think there is no difference, If you upload the form template using stsadm or using the central admin interface and you see the solution admin in central admin, you can see that a new form feature has been added.
So I think it´s the same, but I recomend you to use the uploadformtemplate, looks more specific.
I normally use somenthing like this:
"%STSADM%" -o verifyformtemplate -filename "%FormPath%"
"%STSADM%" -o UploadFormTemplate -filename "%FormPath%"
"%STSADM%" -o execadmsvcjobs
"%STSADM%" -o ActivateFormTemplate -url %SiteUrl% -filename "%FormPath%"
regards.
Alvaro Arias
My SharePoint Blog